They vary widely, and it'll also depend on what else you get with it. I got the bellhousing, flywheel, clutch, shifter, rebuilt tranny for $700. Putting it in a '65 you won't need all of that. Just make sure you know what you're getting! If you don't know, take someone that does with you!
Hey Justin, if you haven't already done so cruise on over to www.vintage-mustang.com and click on the general discussion area. Bunch of helpful guys, many of which have already done the conversion and can tell you everything you need to take into account when performing the swap, etc. Make sure you get the t-5 specifically for the 5.0 and not the 4-banger version. Anywhere from $200-$500 will usually net you one out of a boneyard. If it's a car you plan on keeping a while, I'd cough up the $1,100 for a new one.