I ran into similar problems the other day when doing my struts, I ended up chopping the endlinks in half and removing them from the sway bar side of the thing.
I think I also share the most recent problem, and I think a reason may be because the nut holding everything in place may be 'longer' then the original one making the top piece sit higher. Sometimes this can be a sign of a bad strut mount, but I feel like in our situation it's just a matter of the top piece not being able to go any lower because the nut holding the coilover together (literally) is too tall. This is why that gap may be there.
if i am reading your problem correctly, i think it is because you have the coil spring set low on the coil.. the strut itself is good for a range of height, so when unloaded, the strut will expand.
If you can push it down onto the spring, and they touch (via compressing the strut) then you are fine, it you cannot, then something is wrong.
Ok, now ive got serious problems. Me being the idiot I am, put all the coils on set as low as they go, thinking it is as high as they go... Now Ive got one side about 1" off the ground from the jack point, and the other about 2 1/2", with my jack unable to go under either side, and my factory scissor jack stuck under the side that is 1" off the ground
Hahah, just finally finished. ****sonofabitch that was hard, fronts are too low though, I have 2 options...put the 14" steelies back on, or have my fenders pushed out about 1/2". I DUNNO WAT DO
the fronts aren't the problem its the rear. I couldn't get the rears high enough the fronts were perfect I had the bottom ring 1 1/2 inch from where the threads ended