Well I thought I had my 4wd sorted but I guess not. Little snow today so I put in 4wd, which now requires locking in hubs on my 2093 tracker.  I welded the diff actuator and put in new front cv axles and a 2” lift.  But, now in 4wd it vibes bad over 30mph.  I checked bolts on cv axle and prop shaft and they seem tight.  What did I do?!  Only thing I can imagine is a bad cv joint. 
Runs smooth in 2wd so I know it’s some of the gear for 4wd

Is your back diff mount bolt still in?  If it came out it makes noise as the back of the diff bounces up and down, sometimes hitting the bell housing.  The vibration is the universal joint over flexing.(Just a useful piece of information I came across a few years back.)

Does locking or unlocking the Hubs make a difference in vibration?

Good call on the diff bolt.  I checked and yes all are there.  So, that’s not it.  Other diff brackets look tight.  I should also mention that the right side cv axle was very hard to get back installed.  I had to massage the c clip a lot and now I’m not certain it’s in all the way. 

How much gap should there be between the big hunk of metal on the CV axle and the aluminum diff housing?  I have about 5/16”. 

Okay I tried leaving in 4wd but unlocking hubs, and guess what, vibes gone.  So, it might be the hubs after all, or it just rears it’s head when under power. 
These hubs were adapted samurai and I had to make a spacer 1/4” to make them work, but I don’t see how that could’ve affected the way they work.  The vibe also goes away after 40mph too. 

Do you have the original drive flanges?  If you do, consider installing them for test purposes.

I used the original flanges for the spacers needed to make the samurai hubs work.  So, no, don’t have them.