To percentages, I say take the cash and apply it to your college, or your own startup. Charge them in blocks of hours, and they pay up front for each block. If they can't pay now, they won't want to pay you if the money starts rolling in. Figure $120/hour in 10 or 20 hour blocks, depending on development needs.
To me, the "they had a difficult time finding someone" is a red flag. You should be in a position to fire them as a client without a messy breakup.
If you are considered a part of the startup, make sure you are not putting yourself in an actionable position. If it goes belly up there will be a reckoning in terms of unpaid bills, and the people they owe will go after everyone.
Again...just ramblings. I'm sure others will be a bit more cheery about it :)