Well, if the longer driveshaft came out of one of the cars and it was capable of moving under its own power, then it fits some how or another even if it isn't correct. It could be that the slip yoke was trimmed down a couple inches to get it to sit further up on the trans splines (an old DC racing tip) and/or the rear end was moved back via spring relocation or mismatch.
If it was just thrown in a non running car as part of the deal, then you may have been given the wrong part.
You also mention mixing shafts and yokes. Do you have a mis-match in u-joints? If you have a complete gtx shaft but it is too long, then just have it cut down, rebalanced, and use the yokes that are on it, assuming they are there, of course. If they aren't there, then you need to find one. Also just as an FYI, there are three sizes of u joints out there to use; the large style, the small style, and the conversions joints which has one set of both large and small width caps. Sorry, I can't quote the sizes off the top of my head, but I'm sure someone can chime in with them if needed.,