Good news is, deal is done, and was better than anticipated.

You should anticipate paying more may be close to 500K for estimating purpose. 

A lot more costs than anticipated, but we had a huge margin for error as well.

You might find that there are restrictions you can't live with like prohibitions on parking a camper, boat or commercial vehicle - and even the colors you can paint your doors or shutters.Be sure to ask whether there are any pending lawsuits against the condo association or any special assessments in existence now or anticipated in the future.You shou;d also request a certificate of good standing from the condo association, meaning that the seller doesn't have any outstanding fines or fees. 

Assuming he plans to flip the property after a 6 month rehab I anticipate he will make approx $50,000 - 75,000+ after selling/closing fees.  

If you anticipate making more than 40k per year in profit, you might want to designate S-corp tax status for your LLC.

It was in rougher shape than I anticipated. 

Everything has an anticipated life span but not everyone is going to own the property throughout that entire life span.Roof example, you buy a house with 5-10 yr old roof, you realistically want to hold on to it 10-15 yrs max and then 1031 into something bigger...

I also spent about 3x more than what I anticipated, and I did most of the work myself. 

The percentage will depend on the condition of the home and when you anticipate the next big ticket item will come up.