Yes take a comb through the materials and price them out. Have at least 4 builders price out your project with all the trades. Sometimes GCs that offer a level of self performance like carpentry can avoid double mark ups. Did you see any of the major quotes like excavation, framing, plumbing, etc?
I'm doing a lower level finish. One bid was 60% over budget....another 44%....then with due dillengence we ended up 4% over budget but went with the contractor that was 10% over budget. Pricing wasn't the only varible at the end of the day.
I'd hold the line and get more bids if you can - too much time and money vested - but if the bids come back similar time to cut the cord unless the redesign to meet budget is free.
Q