killer, you CAN build a 5.0L stroker, but it's big $$$. The 4.0L "stroker kit" is nothing more than a 72-89 4.2L (258) crank and rods. The 4.0L uses a 0.10" larger bore than a 258 and 0.44" shorter stroke. Stock bore 4.0L comes out to 4.5L, 0.030" overbore to 4.6L (what I run) and 0.060" over to 4.7L. All 4.0L blocks can't be safely bored to 0.060" and remain reliable due to core shift. If you want a big one have it sonic checked. To go to 5.0L you need to offest grind the crank and get custom pistons (I think the 4.0L rods will still work) at least. A 4.6L AMC/Jeep stroker six is 280 cubic inches.
The 2.8L equipped Cherokees (84-86) won't fit a 4.0L. The firewall on the 4.0L models has about a 2" recess in it. Nothing a good rodder can't fix, but not a direct bolt in. The story from an ex Jeep engineer is that the main design engineeer didn't like the in-line six and intentionally designed the engine compartment so it wouldn't fit. Not sure if AMC had a V-6 on the drawing boards or not, but it's likely (they had a new V-8 design on the boards -- a lot of that went into the Chryco 4.7L, and likely why it was used in a Jeep first). Anyway, the 4.0L was developed and the problem corrected.
So far everyone running the strokers haven't had problems with the D35 axles. At least not on mostly street/trail vehicles. The hard core off road drivers will break them on occasion. but they'll break almost anything given enough time and power. It's tough to break a D60 axle, but I've seen it!!