Late reply, but I have a '66 on an '88. If you build yours, I'd love to hear more. I don't have much advice to offer, as mine was built when I bought it, but I'll describe it as best I can here.
2.9L Engine and all running gear is '88 plus most of the interior - steering wheel; dash and components (except stereo won't fit in the reduced depth of the dash, so elsewhere) AT and manual 4x4 shifter; Eddie Bauer front and rear seats, dash, cargo area panels, etc. all fitted with just the early bronco shell. It even has the seat belt warning bell. Built by an obsessed welder who died before I bought it - he spent a couple of years building - custom made a whole new floor so the seats sit much lower than the EB (tall guys love this), custom shaped fenders so they are cut but do not look like it, massive bumpers, integrated roll cage that doesn't look like one, fuel door, swing-away tire carrier, etc. I can see lots of places where he had to lengthen or shorten things to fit. The whole transfer case linkage assembly, for example, has almost every part cut and welded to fit right.
Most EB guys shake their heads and say he was totally crazy when they look underneath, especially with the 2.9L engine. I use it as a daily driver and on snow covered roads - but not rock crawling - so I like the slightly better mileage, the reliability (I bought it with 40K and now am approaching 90K), the anti-lock brakes, AC, cruise control, etc. with the cute looks and removable top of the EB.