90 Geo Tracker 8v 5spd.  Lifted 3" Calmini suspension.  Warn premium manual locking hubs.
This hunting season I noticed a little noise in the front end a few weeks ago, didn't think anything of it because it only did it up this one hill, and we were driving over broken tree limbs, so I thought it was some limbs hitting the bottom of the car.  Didn't think anything of it.
This weekend it was snowy and icy so I used 4wd a lot more often.  Noise was more prominent.  Basically there is a popping/clunking noise from the front end, only when under load in 4wd.  Not a quiet little clicking noise (like worn CVs might make---CVs are also both brand new axleshafts), but a louder, deeper, clunk that I can feel even in the steering wheel.  You can really feel it in the car and it sounds irregular, like clunk-clunk-pop-quiet-pop-pop-pop-clunk-quiet...intermittent.
The car doesn't lurch at all when this happens, it keeps climbing in a steady forward motion but it really worries me because it never did it before.  Noise occurs when under a heavy load, or 10-15mph.

No noise at all under normal driving conditions (2wd, high or low, hubs unlocked/"free")

No noise when hubs are locked but still in 2wd (I left them locked in on the icy stuff so I could switch into 4wd without getting out to lock them in.  I always unlocked the hubs when I got back on pavement and went any speed past 1st gear!)

No noise in 4wd, high or low, when coasting or applying throttle downhill

I experienced noise only when in 4wd, hubs locked, and applying a load uphill and/or about 10-15mph.  And like I said, it's a real loud clunking noise. 

I never had this problem before, but I just installed a freshly rebuilt t-case with 4.24:1 and twin stick.  Hopefully the gearset was installed correctly, that's an option, but I really highly doubt it because it sounds like it's coming more from the front end.  Also hoping it's not the t-case because I just spent $1,300 on it. 

My mechanic who was hunting with us, said from my description that he thinks it's the hubs locking/unlocking sporatically.  I told him they're new and he said it didn't matter, they could be defective.  I have yet to get under the car and start inspecting everything but I wanted some replies on it in the meantime.
Hopefully my aluminum front end isn't about to grenade itself...

Sounds like a CV going bad.  With a 3" Calmini lift you should have their diff drop brackets, but climbing over limbs if you dropped one side (just a little more) it could be toasted.  Even new CV's just do not last with high angles.  Hope that is what it is, they are much cheaper than any work in the TC.

Trail Tough has such good customer service that I'm almost certain if there was a problem with the case, they'd take care of it...still, I'm hoping it's fine, plus it just doesn't sound like it's coming from the t-case, but from the front end. 

Would CVs make such a loud clunking noise? 
I recall hearing bad CVs before, and they made a quieter clicking noise, this is more of a really really loud CLUNK or POP
Yes, it has the diff drop brackets.  The angles don't look very drastic when the struts are topped out.  Maybe it's my perception, but they don't look as drastic as some I've seen on here (BRD HNTR, such as yours before you modified your a-arms, that angle looked much more drastic than mine).  Plus, it's seen hardly any 4wd, it's been 99% 2wd since I put the axles in.

 You might have a broken tooth on the ring gear. It will do the same thing that you are describing.

Would CVs make such a loud clunking noise? 
I recall hearing bad CVs before, and they made a quieter clicking noise, this is more of a really really loud CLUNK or POP

Last one I broke took out half the cup, and was CLUNKING when moving (but I had the front diff Locked).  Try unlocking the hubs one at a time to see if the noise changes, or becomes frequent.  (i would think) the unlocked hub will turn the CV and not be a noisy as the locked side.  Every one I have busted tore the boot, so was not hard to guess what was wrong.

You might have a broken tooth on the ring gear. It will do the same thing that you are describing.

Lordy I hope not.  As irregular as it sounds, though, I'm thinking it's not.  I can't do diff. work myself or at least never tried

Last one I broke took out half the cup, and was CLUNKING when moving (but I had the front diff Locked).  Try unlocking the hubs one at a time to see if the noise changes, or becomes frequent.  (i would think) the unlocked hub will turn the CV and not be a noisy as the locked side.  Every one I have busted tore the boot, so was not hard to guess what was wrong.

Still haven't had a chance to check it out/been driving another vehicle all week too.  I guess I have some looking around to do first, I'll check back with any questions/what I found

Bad Cvs in the half shafts on my truck sounded like a roller coaster when you climb
the hill before you go over, click, click click, at regular intervals

Wild

How about this to stump you:
with all four tires on the ground, parked, I lock my hubs and try to turn my front axles by hand.  With the hubs locked and the tires on the ground, the axle shouldn't rotate anywhere, but it sure has a lot of slack when I try to rotate it back and forth. 
Is this normal or could this be excessive clearance inside the hub?

No, it's not the hubs, so long as they are working right, but it could be your
CVs are shot, the same reason you have a lot of noise in 4WD also, I have seen
broken cages inside the CV that lets the ball bearings move around too much.

I say get some new CVs and go from there

Wild

Update: not the hubs. Took them off and in to 4wheel parts for warranty exchange and he couldn't trade them without finding anything wrong with them. Which we couldn't. Any suggestions? I think it will go to the mechanic tomorrow. No time to brainstorm...
If the whole thing is shot it will be time for the GV banjo and third or the Anvil.
Or if I get really pissed and start gutting everything I'm looking at the new Calmini kit for the front. Already got the rear half done. Cheaper than trailslayer.
I just read a post about a Low Range SAS. I am really interested to see if that makes it to actual production and start to sell

I will keep this post updated once the problem is found and repaired.
We test drove it around yesterday and realized that there is almost no noise coming from the driver's front, but VERY loud at the passenger's side front.  That jogged my memory, and I remembered that when I dropped the oil pan, we ended up removing the front diff with the pass. side axle still connected.  Maybe doing that over-extended that CV joint?  We'll see. 

As far as the oil leak, my mech. is checking that out too.  Looks like the front seal.  If so, I'm just going to have it done.  No time to do it myself.  What really sucks is I just had the timing belt replaced 3,000 miles ago and that would have been the best time to do the front seal while the timing assy was out.  Oh well

Dj, that really sounds like a grenaded CV on that side. If you can grab hold of it while parked and try and move it around it may slide in and out a bit but shouldn't twist at all. (With the hubs locked and in 4wd)

It doesn't twist at all, but either side hubs locked the axles feel like they had a little slop.  But if both were the same then that led me to believe that was normal...especially since I locked the hubs on my parts car and tried to move the axles and they felt the same.
Today, he told me that he traced the noise to either the differential or that inner CV joint.  He believes more that it is the CV axle.  Makes sense if it was over-extended when I left it connected to the front diff as I moved it out of the way of the oil pan.

Aren't pass. CVs notoriously weaker than driver's side?

Sounds dumb, but go for the easy/obvious stuff first,  check all the bolts/bushings holding the front diff,  I'd be willing to bet one's worn out.   One question, did you do the widening to the control arms?  Possible loose bolt there?