i don't think you will have problems because of driveshaft alignment. here's the recipe for what i would do with that yj for cheap. and i'm a cheap bastard.

1. waggy front with 5 on 5.5 conversion. approx. $300

2. waggy front springs. $50? free?

3. yj rear springs and traction link(no clue on price for anti wrap bar, i built mine out of tube laying around. springs shouldn't cost much if you have to buy them).

4. diamond plate corners and tj flares will be about $200 if you find deals.

5. steering for soa can get very expensive. research what it takes before you go soa. it can get spendy depending on what you need to buy. a basic bolt on, everything you need kit will probably push $1000.

you have a lot of choices to make. just make sure your money and time goes to upgrades, not lateral moves or downgrades.