Sorry for the delayed response. Thank you for your comments Saphroneth, its never too late for a critique. You seem to have a great grasp on Civil War history. Assuming you points are accurate I don't really have a rebuttal. However, I certainly don't plan on overhauling the POD. My question to you is... Do you see the Union winning the Peninsula Campaign under any circumstances?
Yes, at least three even without removing McClellan or changing Confederate plans.
(1) McClellan gets all the troops he wanted from the beginning (so McDowell's corps, Wool's division and possibly Blenker's division). He can turn Gloucester Point with an amphibious landing, thus breaking through Yorktown weeks earlier, and all else being equal batters through the defences of Richmond in May or June. (Though not in early June itself, the rains were terrible.) A variant on this leading to the same timing of the result is that McClellan has McDowell's corps complete with shipping in early May, as this way he can land an entire corps at Eltham's Landing in one lift and "bag" the Yorktown garrison or some of it - OTL he had only one division of shipping and so his buildup at Elthams was too slow.
(2) McClellan is sent McDowell's corps in early June like he was promised, either overland or by sea. This means he can protect his flank when he advances on Richmond. If the CSA launches the Seven Days battles they run into about five divisions instead of two, while McClellan emplaces artillery in the last few days of June and blasts his way into Richmond in early July.
(3) McClellan is sent the reinforcements he was promised post-Seven Days, which amounted to about 55,000 AP&A (so another ~20,000-25,000 effectives). Thus now actually with a reasonable numerical advantage, he advances up the James clearing Confederate batteries and mounting regular approaches on Petersburg. Union gunboats come with him, and he goes post by post up the James until he reaches Richmond, probably some time in August or September.
Those all rely on more troops to McClellan, but there is another option which doesn't:
(4) The line doesn't crack at Glendale, possibly because Franklin gets enough sleep. McClellan shifts supply to Harrisons Landing and fortifies successfully, using the Chickahominy and White Oak Swamp as a flank guard, and Pope comes down through northern Virginia.
With McClellan right there less than a day's march from Richmond Lee can't possibly divert enough force to actually
stop Pope, and by mid-July both Union armies are able to catch Richmond in a vise.
So yes, the Peninsular Campaign is eminently winnable, the problem was simply getting McClellan enough resources (or, of course, whoever replaces him). During the Seven Days, in Effectives terms (and correcting a couple of mistakes made by Livermore in his conversions) there were about 70-80K Union "Effectives" - obviously the number goes down as casualties are suffered - and at Glendale when the Union had 73,500 Effectives the Confederacy had about 91,300. Killing/crippling McClellan doesn't change that the Confederacy really did have a preponderance of resources available during the Seven Days, and indeed McClellan's performance was very good - he's one of the only Union generals able to fight regular approaches (and perhaps the only one able to do both that and control an army of over 100,000 Present), and he was good enough at it that Lee felt that "McClellan" plus "supplies" near Richmond was something to be avoided at all costs.