I would not think twice, if its not a #'s matching show car then go for it, my next super bee build is going to be a disc brake, fuel injected 440, a/c, automatic, with all digital gauges, what ever color paint I feel like shooting it with, big thick aftermarket wheels in the back, track suspension, and new custom seats, that look sporty but feel like a couch..
I say go for it, one thing I will tell you though that I learned from doing 4- 6.0/4l80e conversions, over 6 tune port and LT1 conversions, and 1 5.0HO/tremec install. Take it ALL out of the donor, I mean everything, from the tank unit and wiring all the way to the fans, and cluster. Take all the exhaust components, all the harnesses (power seats, power windows, day/night light sensor on the dash, etc etc etc...
I took a 6.0 4l80e (2wd) out of a loaded crew cab truck, it was tagged in the rear. I ended up using the power seat system harness and all, the day night sensor, the rear view mirror, the nav, back up camera, everything. It all went into a 39/40 tudor, it looked intimidating at first, but after I started running it all it started to feel like it belonged there, I had to make some wires shorter and some longer here and there, I had to have a tank custom welded to take the 6.0 fuel unit, I know I could have just put an external pump, but I wanted it to be so that if there was an issue mechanically there was nothing special needed, just say 2004 gmc sierra and give them the vin number to the truck.
One Problem I did have was the abs and air bag system, I used a billet column, I thought about getting the truck column to fit but it was way off in measurements and it was an ugly unit too. So I used the harness and figured what wires went where to get my billet column to work. The abs I could not get to work because I was not using the axles, I looked into it and it was not going to work, I had the dealership go into the computer and gt rid of the warning light, cost me $350 for them to do the research and get it done, but the abs light never came on and it stopped going into limp mode, which it was doing before we fixed it...
But anyway, take it all, you dont know what you will need, you can always just apinless wire it, but having all them harnesses will pay off at some point in the build..