I've got pretty much that exact MJ...4.0L, 5 spd, SOA, 8.8, 4.10's, 33's etc...it's a popular setup.
The 4.10's are close to stock with 33's, maybe a little high, I don't use 5th too much on the highway but otherwise fine for daily driving and of-road.
SOA on an 8.8 will give you more lift because of thicker tubes than a D35, 6" coils up front should match well. I've got Rubicon 5.5" XJ coils with a slight bit of forward rake.
Only thing I did differently is I went with a '96 XJ D30 that had stock 4.10's, non-disconnect and comes with the larger 297-X u-joints...also I got lucky and had an AX-15 in my '89