Im looking into lowering my 97 FLSTS in the rear . Any one know any thing about good options or pitfalls

FLSTS - is that a Springer?? I don't know much about lowering Softys, but am about to take my Dyna down from 12.5 inches (stock height) to 11 inches at rear. Have a good look under your rear guard before you lower so you can see if there are any bolts from the indicator mounts, seat bolt or tail light wiring that the tyre could hit if it bottoms out. I may have some probs because instead of the 160mm tyre it came with I have a 180, so clearance on either side is very tight - only mm's to spare! I think the stock rear tyre on your bike was around 150mm wide, so you should be right on either side for clearance.
One way to check is to undo the shocks and lower the bike onto the tyre to get an idea of how it will work - easy on a Dyna but not so for a Softail I guess!
The other thing to remember is that if you go to a very low rear, you may need to replace the kick stand as well - you may no longer have the room to swing it out. You are also changing the fork rake, so steering may handle differently.
Good luck! It will look better, and if you are a short arse like me you get your bum closer to the ground, so the bike is easier to move around when parking. : )

I used the lowering bolts. It is set on the highest low setting and drops the ride height by about an inch and a 1/4. Looks good, still able to carry a heavy pillion an was ok on the recent trip to Darwin. It is the most cost effective way to go.