First of all, some speed drop in colder weather is inevitable, so if that was your only problem I wouldn't be too concerned. Pain is another matter. I would suspect the problem may be in the positioning of your cleats or saddle. A bigger shoe may have your foot position changed if you positioned the cleat in the same spot it was on a smaller shoe. You need to fit the position of the cleat for each individual shoe. Also check the thicknes of the sole of your shoe, winter shoes often have thicker soles and may need an adjustment in saddle height. Likewise, the added layers for cold weather riding may mean you need to adjust your saddle position, usually down & back a tiny amount. The added layers may change your riding dynamics and you just may be using a slightly different set of muscles, as you suggested but you may also be bumping your thighs against the handlebar more than you realize.