Changing two things at once like this can really make it hard to see what's happening. However, I think your main thing is you just don't have the same gear ratio changes available to you in the places you need them. When cruising now, you might not be able to get that gear ratio that allows you to put out your optimum wattage at a torque you can maintain with your muscles.
Do you know what gear ratios you where using the most with your previous set up? Can you get the same ratios with your current setup? Would changing to a different cassette get you those ratios back?