Your engine/tranny may or may not fit. It would help to know what it is.

Probably not on the driveshafs as typically fullsize Waggie springs extend wheelbase 2" per end (probably why the wheelwells are hacked). Waggie springs are already 2" taller than CJ springs, so you add the 3" you mention and there's even more distance from yoke to yoke. A tape measure would tell for sure though.

You're correct about the problem with the front shackles. Keep in mind, however, that if there's no engine in the frame now (assuming there isn't) that the weight of the engine/tranny/tcase will extend the springs and push the shackles forward. Common sense stuff.

The CJ tub (assuming it's a CJ7) will fit the YJ frame. Lots of people put YJ tubs on CJ7's, so do some google searching, see how it's done, and do a 180 on some procedures since you're going the other way.