So I am in the process of lifting my 89 xj either 3'', or about 5'' with 2'' pucks and 1.75 or 2'' shackles in the back. We went to a local liftkit/offroading place today, and the guy told me basically if I went above 4'' I needed to be prepared to spend big bucks on a full SYE, over the knuckle steering, the works.

My question is: If I use the 3'' kit, 2'' spacers and shackles, for a total of 5'', then add a front bumper and winch, and a rear bumper, where will I be as far as lift? like 4''?

Weight will make it sag, but it depends on how much it all weighs. And not all 3" coils give you 3"..most give more.
Honest opinion here, Re 3.5 lift kit gives around 4-4.5..once you add weight to it, it'll sag to around 3.5-4". Seems to be what your after.

Before adding the winch/bumper let it settle a bit then put your accessories on, then see where you're at. you can always add 3/4" or so spacers to level if needed.

I got the 3'' rc coils, quick swaybar discos and xj leaf packs with the aal from a 92 xj in the junkyard. I called rc, and told them the shocks on it were yellow, and they were like, "wow that is old''.

He also said without all the stuff in my op, at 5'' I would be all over the road.

I know I still need a pair of Lca's, even at 3''. What else do I need if Install the 2'' pucks and 1.5'' shackles? when I put a winch bumper and winch, I should end up around 4.5'' correct? at 4.5'', I should be good with just a t case drop, being an 89.

Also, can I run shocks for 5-6'' lift on a 3 or 4.5? I found a good deal on some, and Im considering returning my rc nitros.