Were your short arms factory still?
Aside from your suspension and lockers and tires etc. what's the best thing you've done to your zj? Good overland changes to help out new zj owners perhaps?
I believe the lower were Rubicon Express Super Ride adjustables. Factory uppers in the front, RE adjustable uppers in the rear. It was a long time ago though, so not 100% sure I'm remembering right.
I wouldn't get too hung up on lockers, especially if you still have the 35 in the back. Can't remember if you have it still or not, but it's a matter of when, not if, it will break. An 8.8 is an easy swap, as is a HP30 from an XJ. I run that axle combo, V8, 35" KM2's, open front, Aussie in the rear, and it gets me just about anywhere I want to go, and further than most want to take a full bodied rig.
Not sure which t-case you have, but if it's the 249 (QuadraTrac) definitely ditch that for a 231 (CommandTrac) or a 242 (SelecTrac). I've run all 3 and prefer a 231, but currently have a 242 in my 5.9. I chose a 242 over a 231 there only because it was literally sitting on the ground at the u pull yard.
If you weigh the rig down with a bunch of cool overlanding gear, the 4.0 will struggle more than it already does. My dad has a 97 ZJ with the 4.0 and it's almost pathetic how little power it has compared to my 5.2. I'm not up to date on 4.0 power adders, but if you add weight, I'd add some power too.
I know you asked for things besides suspension, but long arms really are a game changer on a ZJ. Increased reliability due to beefier mounting points, substantially better ride quality on and off road, and most kits help with overall unibody strength too. My ZJ rides much smoother on the trails than my wife's JKU that's equipped with similar tires and shocks. If you ever go above 3.5 to 4" of lift, I would almost call long arms a necessity too.
Keep an eye on steering box mounts. The tab for the rearward ear on the box likes to break off. Some have fixed with 4 bolt Waggy boxes, others use steering braces, I use both.
ZJs have been around long enough where if you can think of it, and it's a good idea, it's been done. If it's a bad idea, someone has done it too. LOTS of good info on some of the ZJ specific forums out there too.