Will you use a general contractor? - Add about 15%
Will you use an architect?
Will you be making dramatic structural changes?
What degree of quality of materials will you use? (This is a biggy);
How fast will the project move? (This affects carrying costs which can be substantial).
A general range: $75/sf for very basic renovations with no general contractor and no architect ranging easily up to $180s.f if you start getting fancy with quality. I primarily only do mortgages now but happy to answer you questions. John 617-340-9647
If you're not well versed in construction, absolutely bring your contractor with you. If you're purchasing a 5000 sq' rehab, you will definitely want to go with high-end finishes. If you plan on going the Home Depot/Lowes route, do not take the project on.
I would lean more toward the $300 per sq' to cover incidentals. Golden rule in construction: set your budget and then double it because that's where you'll be at the end of the day.
Best of luck
Your cost per square foot would be less because the more expensive items are kitchens and baths. Kitchens, especially. And you've only got one of those (usually) per house. So while you might spend $30,000 for a gut rehab of a kitchen in a 1,500 sq. ft. house, you might only spend $50,000 on a slightly larger kitchen in a 5,000 sq. ft. house.
Be sure to interview several (the recommended number is three or more) contractors. You'll find prices vary greatly. With a rehab I'm just finishing up, I received quotes of $45,000, $65,000, and $155,000 on the same house.
Hope that helps.