ok here is the deal, I have boondox 3 inch coil lift 4 door springs in my 2 door tracker (Stock struts) with 2inch strut extenders, and flipped strut mount.  I am wondering would it be to much to put a 1/2 inch strut mount spacer in there? I mean would I have to much downtravel do you think?

any easy way to tell? 

It depends on your definition of easy. When I did mine I jacked up the front and removed the wheel. I removed the FWH and the circlip from behind it. Then I removed the lower strut mounting bolts and slid the hub down through the strut mounting and clamped it in the equivalent position. Then you can check for binding at which point the driveshaft will start to pull back through the hub.  You might need to pull on the end of the shaft a bit if the boots over the CV cause it to pull back. Remember to swing the steering through its entire lock and watch out for the shaft dropping into the splines in the CVs and giving a false reading.

All this with stock struts?

Sounds like too much to me.

Sounds close to what I've been running

4dr coils, 1" coil spacers, 2" strut spacers (no strut flip tho)

If I get it cranked around an a tire drooping ... pop goes a CV. (I'm also locked up front)

Before I did the 4dr coils tho I never had a problem. The 4dr coils shouldn''t change droop, but I think the added rate helps to extend the CV that extra bit to pop them.

Next time I'm under it (changing another CV no doubt), I'm going back to the 2dr springs.