I have a 1998 and I had the same dilema. I'll give you my experience.
I wanted the RE 3.5 super flex - learned a lot about it, studied reviews...
I found a RE 3.5 kit used for sale.
Key Parts:
3.5 coils
3.5 leaf springs
Lower Control Arms.
Variable Parts: (can be multiple vendors/design)
Extended Brake lines - YJ oem lines work well and are cheap (rockauto.com)
Track Bar - don't re drill the mount. Spend the cash, get a good double sheer.
Sway Bar Disconnects - I like JKS
Front Bump Stops - hockey pucks FTW
Rear Bump stops - Daystar Part and eventually a contact plate on axle.
Shocks:
Get what you pay for. I'm testing out the ZONE nitro next week. But obviously Bilstein or OME etc are best. Try to calculate actual size requirements, compressed and droop the "average" lift size charts can be off.
SYE:
Consensus is 1997-2001 need them. I'm installing the IRO hack n tap next week also. Get the correct shims to orient the pinion angle.
To Make this a 4.5 lift, add upper control arms, longer coils (or spacer) and a JKS shackle to the leaves. Once you go higher, you'll want larger tires...Now you need gears, and heck why not lockers....
It's an inverted pyramid. The top is the coolest, but most expensive and custom.:confused1