Raised Crossmember?

To start off I built a new crossmember that raised the transmission mount up roughly 1/2". N

ow when starting to drive in first gear I have a thumping sound that will hit once or twice then go away through the rest of the gears. Ive looked underneath the Jeep and nothing seems to be hitting whatsoever (thats why I built it to be where its at). A friend thinks its a problem with the rear output of the transfer case being at more of an angle? But I personallly do not. Anyone else ever had a problem like this or have any ideas.

93 w/AX-15 and currently sitting with 3" lift

Do you have an SYE installed?

check where your exhaust runs over the crossmember.
mine will somtimes knock a few time when i start it or put it in drive

Which would lead me to believe the culprit would be motor mounts?!

No I do not have an SYE (well I do just not installed yet). And the exhaust is okay I think, I put a couple bends in it to get it up out of the way. So im pretty sure it is not that. The sound is a relatively loud thud if that makes any sense.

My tranny has been thumping around for two years now. Recently got a new tranny mount, thumping gone.

mine started after i changed the motor mounts and also installed a header but a little help from the bottle jack moved it up out of the way.

I replaced the tranny mount already, and the motor mounts seem good but im not one hundred percent sure. One thing to add is that I drove it down my drive way in front wheel drive only and there was no sound what so ever.

You said you have no SYE and it's lifted 3".... It could easily be your rear DS binding up due to excessive angles, especially since you raised your T-case. Not to mention the fact it isn't there with the rear DS removed. Get that SYE and CV shaft and I'd bet it goes away.