For my lift I am planning on cranking the torsion bars/ball joint flip up front and springs/spacers in the rear.
Sounds fine, that is what I will be doing to my Trooper before too long...to fit 35s (with a little sheet metal trimming that is <img src="/forums/images/graemlins/notooth.gif" alt="" /> ).

I already have Edlebrock shocks all around, but will probably need to replace them or get shock extensions for the front/replace the rears. Does this sound good?
If the shocks aren't worn I would keep them. You could put a small spacer on the front like this. On the rear you can gain an inch or so of droop with longer shocks, but you have plenty of rear flex to start with on a 2nd gen Trooper...and you have to be careful of the brake lines, may need longer ones with longer shocks. Put some Indy4x brake lines on your Xmas list <img src="/forums/images/graemlins/wink.gif" alt="" /> And, you may also need to extend the bumpstops to keep the longer shocks from bottoming out. You'll have to decide if it is worth it to you...

On the 33x12.5 tires, would they stick out? If so, any ideas how much? Just wondering if I need to buy flares or not.
If you are uing Isuzu wheels they won't stick out much at all. You won't need flares. Now with the 2" backspacing wheels I am going to put on <img src="/forums/images/graemlins/rolleyes.gif" alt="" />...flares might be necessary but we'll see.