Driveshaft Clincking Sound Under Torque

Hello all. I'm new to the forum.

I have a 2002 Taco XtraCab V6 5 spd 4x4 TRD and for the past couple of months I've been having a clincking sound in the driveline when letting out the clutch pedal. First thing I thought was the u-joints as it was the same sound when my u-joints were going out in another truck I used to have. My truck has 292k miles and I figured it was time for new u-joints. So I had a new driveshaft made with 1310 u-joints, new CV, and new center bearing and just got done bolting it in. The sound continues, but the pitch is slightly duller. It still has that higher pitched tinny sound.

While the driveline was out getting built, I drove around in FWD (factory open front diff) and I didn't hear any sounds. While I was under the truck, I noticed that the transmission mount is missing 3 of the 4 bolts. I bought new bolts, but I didn't have a jack handy to help realign the bolt holes. I'll save that for another day and will throw a new mount in while I'm at it.

I was looking around to see if there could be anything else hitting the shaft or the exhaust pipe, but didn't see anything. With the truck parked in gear, I tried forcefully rotating the driveshaft back and forth to check the slop and I was able to recreate the sound in the driveshaft.

So my question is, does my transmission or my transfer case need to be rebuilt? Now that I think about it, I should have checked the slop in the rear differential before bolting the driveshaft up.

Thanks in advance. Cheers