First, if Britain truly signs peace in mid-1940, no Balkans, Mussolini will be given his pound of flesh from French territory and colonies and will be busy assembling troops to take part in the anti-bolshevik crusade, or even if sends an ultimatum to Greece, without British help, the Greeks will rush to grant him anything. Ditto for Jugoslavia entering the Triparite PAct. Not to do so would be suicidal. This means the Wehrmacht can attack the moment they prefer, enough time to take the pocket and turn towards Moscow earlier before winter.
Why is Vichy France accepting large concessions to Italy? They're beaten, but not yet complete tools; if Hitler does hand "Il Musse" Nice and Savoy, for example, or Tunisia, that'll make them angry, even if they can't resist directly. Hitler was (being him) pretty nice to Vichy at first, because he wanted a stable puppet, not an occupied state in rebellion (and, from what we see of Vichy, it mostly worked). Why does he reconsider drastically because Britain is beaten? He thought they were already when he made the decision IOTL.
Why is Yugoslavia more willing to support Germany here than IOTL? They're actually better off for British guarantees; remember, Britain has a negotiated peace, not an unconditioal surrender. If the British recognise the new Yugoslavian government and promise it protection, they're better off than they were IOTL, as Hitler will at least consider not wanting trouble from Britain again. And as noted, Britain will be in a "Cold War" at best with Germany; they'll guarantee the independence of anyone that's still independent.
(I suppose you could argue that the Yugoslavian coup wouldn't be sponsored by Britain with Halifax in charge, and thus might not go off, but that's no certainty, especially with Churchill still in the government.)
Likewise, why won't Britain defend Greece's neutrality under these circumstances, assuming that Mussolini would even dare mess with them for fear of provoking a conflict with Britain (he was much more cautious than Adolph)? Hell, I could make the case that Romania and Bulgaria wouldn't join the Axis here if there are believable British guarantees made for them;at the very least, Hitler might thread a little more carefully around them a little longer.
Finally, how much earlier do you intend the Germans to attack the USSR? The original starting date is a dream, what with the spring flood and all. The best you could hope for is probably something in early June, and a couple of weeks might not make all the difference between victory and defeat.
Second, in this scenario, I expect army-size expedition corps from Spain, Italy, and Vichy France. Even Turkey joining the Axis is not unreasonable by this point, if Hitler promises them the West Caucasus (he wanted the Baku oil and Ukraine). Even more troops for the Axis.
Turkey was very neutral, so it's not all that likely that they join, and the value of their forces in a modern war is doubtful; at best, they could serve as occupation/anti-partisan troops. Likewise, the Italian divisions were a mess - too small, too little artillery and support, bad armour throughout; some units like the Alpini were good, but most were mediocre or worse - and Vichy France wasn't allowed an army under the terms; in any case, the Germans used their equipment to good effect themselves.
This brings us back to the point Michele usually raises, and may already have, here (as you know, there are a couple of different threads on this topic right now): the Germans' major problem was never manpower, but equipment and materiel. Volkssturm? Think of Enemy at the Gates, that's what it was like - "You there! Here's a brassard and a rifle! You - here's a brassard and the ammo, don't go too far from the guy with the rifle!"
Third, logistics is not a God-given physical constant: more Axis manpower means more personnel to clear, build, and adapt railroads. And more troops to clear the partisans.
But the troops will themselves need to be supplied, making the situation worse in the short run, even if it does improve in the long run (you're somewhat aware, I take it, of the time it takes to build roads - it isn't done in weeks, or even months in most cases). Railroad is an ever bigger bitch, and on top of that there's a German lack of trains and rolling stock.
Fourth: with more troops, and more weapons and equipment since no war production would have been wasted for a naval campaign against Britain, the Germans are in a far better position to occupy the whole of Ukraine and reach Moscow, and withstand Zhukov's counterattack. Truly, contending Moscow will be a urban house-by-house hell, but nowhere as bad as Stalingrad, since the Russians won't have a major river at their backs. Zhukov's counterattack will be the Russians racking the (momentary) bottom of their manpower barrel, before the 1942 conscripts rush in (and less of them, since the Axis is in Moscow and on the Don).
The real industrial drain for Germany that the Navy was responsible for was the surface ships (esp prestige projects - heavy ships like the Tirpitz), and those wouldn't have been called off just like that. The surface fleet orders were pretty stable; what increased was U-boat production. You could take away some, or even most, of that, I suppose. Still, it's not a huge boon, especially as one must take into account that production lines aren't retooled that easily; a naval yard can't necessarily build tanks, for example, or at the very least not right away.
As noted above, I strongly doubt that both the Ukraine AND Moscow could be taken in the same campaign; even allowing for increased manpower, there are other limits. Light infantry isn't good for much if it isn't supported by something more solid, and it certainly isn't strategically fast if it goes on foot. And I think you're seriously underestimating the time it'd take to take Moscow; IOTL, they barely got there at all in 1941. How long do you think the Germans would have to batter it before it gave in? Not as Stalingrad, you say (I'd disagree, Moscow being bigger and better defended), but what, then? A month or two? That's still time for them to freeze and Zhukov to counter-attack.
Even if Zhukov's counterattack stops the pressure on Moscow momentarily, it will push the Germans much less further away, with more troops and equipment the Germans are poised to finish the job in Spring 1942 admitting the counterattack really succeeds. If Turkey is Axis, major front in the Caucasus, so no troops for Zhukov, goodbye Moscow. In this scenario, Hitler is suffering no blockade, so he has more access to oil, so he is less anxious to get Baku at the expense of Moscow. OTOH, admittedly, if Turkey is attacking from the south, going for the Caucasus makes somewhat more sense. Losing Baku would still be a severe loss for the URSS, but quite proabably noot so bad as losing Moscow and the Russian heartland.
Contrary to the Draka books, the Caucasus is not easily invaded from the South, with its mountainous terrain; that front isn't mentioned much in the histories, but was about as hopeless as Italy in WWI. Turkey's outdated army would not bind up any comparatively large RKKA divisions. As for oil, Hitler might well find himself in less supply here, as he can't bully Romania into selling Germany its full production on credit. Romania and Hungary might well demand cash for their products, or other securities, and if Hitler fucks with them the British blockade is back in action. Mussolini might transit oil throuh for him, but will it make up for everything that's lost?
People in the West tend to miss how much of a rout the Winter Offensive really was. The Germans weren't retreating, they were fleeing; only Hitler's stand-firm orders (much-despised in later contexts, but very useful there) prevented an all-out collapse. In addition, much heavy equipment was lost there that couldn't really be replaced (Germany STILL wasn't at full war production by then); Speer lies a lot, but there he was right.
Fifth: Kalkin Gol or no Kalkin Gol, in this scenario, it makes rather more sense for the Japanese to backstab a weakened Russia with a two-front war than picking a war with a British Empire and a USA which can direct theri whole intact combined might against them. Whereas, in 1941 the URSS can spare no troops in the Far East besides the ones already garrisoning the border. Whereas the Japanese have no such problem. If the Japanese attack, no Zhukov counterattack, so Moscow eventually falls (house-by-house figthing are costly, but without a relief, the defenders ultiamtely fail). No Moscow, and a two-front war, the URSS is KO.
Not that the Japanese Army was very good on the ground (training poor, small arms poor, armour and artillery abysmal), but all right, let's say they mount a major offensive and manage to defeat the local garrisons. Now what? They have an even worse logistics nightmare to contend with than the Germans and suffer the full consequences of winter attack in arctic climate. Not pretty. In addition, Stalin never commanded ALL the Siberian divisions to Moscow; the Soviet Far Eastern Command was essentially self-contained, and while it sent reinforcements to the West, it was never broken up.
And, if worst comes to worst, what'll Stalin do; does he consider the Far East more valuable than Moscow? No. "Fuck this, Georgy Konstantinovich, get everything you can over here now! If the Japanese monkey-men want the frozen tundra, they can have it. For a couple of years, at least..."
The Germans don't need to conquer ALL of the URSS. They just need to take Ukraine, Moscow, and the Russian heartland, up to the Volga. Without these, Russia has neither the manpower nor the industrial potential to continue any serious conventional war with the Greater German Reich with Siberia and Central Asia (not to mention the Japaneese would be truly stupid not to seize Outer Manchuria and Eastern Siberia, so the Soviet Rump will only have Western Siberia and Central Asia, admitting the latter's nationalists don't get funny ideas..). It quickly becomes a mop-up operation from the Volga to the Urals. At that point, either the Russians beg for peace, or it becomes a long-term Vietnam-style guerrilla war on the Urals between the Siberian rump (which by now will be down to a regional power as manpower and industry goes). Quite probably a big cumulative attrition headache for the Wehrmacht in a decade or two, but conventional war is essentially over.
I think you underestimate the Urals factories. And regardless, the Germans can't reasonably achieve all that (beginning at the start; they have enough forces to take EITHER Moscow or the Ukraine, and not be certain of it at that) even so.