Very strange clunking from driver side tire - everything tried so far no go? (2007)

[KorJax]

So, I just bought a 2007 manual yaris and go figure the clutch went out a month later. Car was perfectly fine otherwise, except for some iffy braking. Some mechanic friends of mine offered to help me out, so I bought a clutch kit and we put it on. Turns out, the brake pads were really bad and so were the roaters, so I ended up getting those replaced too.

New clutch works great! Brakes are solid. Except, there's a really strange issue that has now come up that has us all confused. ONLY when the car is driving forward from a stop at low RPM, a very hard "THUNK THUNK THUNK" sound happens from the driver side wheel. It noticeably judders the whole car and I feel it in the gas pedal. It could originate somewhere else and just "vibrate out" from the wheel for all we know, but that's all that happens. Cruising? Totally fine. Accelerating from a stop at higher RPM's (lead footing)? Totally fine. Only when the engine is "working" from a stop so to speak do I get this serious clunking. After we replaced everything it used to do it when braking too but that stopped after a while (for some reason).

We tried testing out the transmission, seeing if it got damaged during install. Nope, tests showed it worked fine. The issue also never happens when the car is jacked up - the wheels rotate just fine, the brakes brake just fine, etc. Everything spins and runs as it should as if there were no issues. So then we thought it might be a problem with a driver side driveshaft since it had to get taken off at a weird angle, so they were concerned it might have been damaged. Bought a new drive shaft, put it on, works fine while jacked up. Issue still remained.

Then, we figured it had to be the engine mounts, which were really fucked up. We figured it was likely that because the mounts were bad, the brand new stiff clutch is just causing the engine to buck under strain from a stop. Engine mounts replaced, all shiny a new. Issue still remains.

At this point we are at a total loss. We even brought over a mechancial engineer friend and he had no idea what was going on, thinking that there had to just be a loose/missing bolt somewhere, but we double checked everything and reseated what we could to no avail.

One of my friends thinks that there might have been an underlying issue this entire time that I couldn't see because the previous clutch was so bad that the engine never had the torque to cause the issue to happen in the first place. I'm just wondering if this is the case, what it could possibly be.

I'm also thinking if the brand new clutch and rotors+pads need time to be broken in. On our first test run I also got the issue when braking (likely from the strain braking had on the wheel) but haven't had it since then. The calipers weren't in super solid condition but they weren't bad either. I'm not sure if this is a clutch issue or what.

What could it be? For now, the car is totally drivable, I just have to make sure to give a bit higher RPM than I normally would on stop avoid the hard clunking/juddering on I feel in my driver side wheel and in the pedal. At least one good thing out of all of this is the amount of shiny new parts in my engine bay now lol