Unless its a rusty mess, $4k isn't a bad price for a '71 Challenger, even if it isn't a real R/T.
You'll spend way more than $900 rebuilding the 440. WAY MORE. Even a stock rebuild will set you back more than that in parts, plus machining costs, balancing, assembly etc. I'd think you'd be lucky to get a 440 built for under $3.5k.
Rust is going to be a big deal. If it needs floors, make sure you check every part of the car for rust. Every panel that needs to be replaced adds hundreds of dollars to the repair costs just in parts. Be sure the frame rails are solid. If they aren't its a huge added expense.
Sounds like you may be missing a lot of parts. May not seem like a lot, but when you start putting it back together you'll find that you're missing twice as many things as you thought. It's VERY easy to get nickel and dimed to death with small parts.
If you're worried about it being a real R/T, make sure you check the fender tag. If it doesn't have one, or any buildsheets, assume its not an R/T. Even if it was, without those items you'll probably never prove it was. Again, depending on the condition of the car, $4k isn't a bad price for a '71 at all, even one needing an engine, trans, and floors. '71 is a popular year, and if it was a big block car, it's worth some money. Even less popular Challengers would get that much for a clean shell.
Make sure all the VIN numbers match, dash, fender tag if present, door sticker if present, cowl, radiator shroud, there's a few other places.
Figure out how you're going to title it BEFORE you buy it. Does your friend have a clear title? Or is it going to be a bill of sale? Find out what you need in your state, buying a project and then finding out you can't title it is no fun. Even straightforward transactions can be a pain at the DMV, so make sure you get all the right paperwork.
Enough of the bad news, good luck! Sounds like you may have quite a find on your hands if it really is a '71 R/T!