I would think that clunking sounds would not indicate a bad bearing. I would expect a bearing to grind when it's going out. I don't know but it might be an indication of some looseness or misalignment of the stub axle assembly. On the other hand, it sounds more like a U-joint. But you say they have all been recently changed. I would still check them first.
I'm certainly no expert on transaxles and I don't have a theory about what in them would cause a clunking but if you heard that before your old one went, you'd have more insight into what it could be. For that reason, I would also be cautious about discounting the tranny. Other than when it's warmed up when do you get the clunking? On a gear change? Coasting? You say it's new. I looked back at your previous posts about your tranny and I'm a little confused at how you know it's new. Did the PO tell you that? Was it recently rebuilt?
With regards to your uprights and bearings:
The bearings in the uprights are standard parts available from any bearing house. I didn't consider the nut that difficult to take off but you will need heat to take the hub off the stub axle. I disassembled mine a long time ago and as I remember, the manual suggested heating the upright with hot water to get the bearings out. Check the manual to make sure.
I don't consider myself to be particularly skilled and it seemed to come apart and go back together pretty well. Read the manual and follow what it says. I would make sure you have a hardened spacer (you can check it with a file). If the spacers are original, they won't be. Get hardened ones from r.d. enterprises, DBE, or Richard. I doubt they would sell you any that weren't hardened but make sure.
When assembling, you must use the correct Loktite (635) on the splines of the stub axle and hub. r.d. enterprises sells small quantities of it.
The thing you might want to be aware of is that the stub axle is not itself hardened. Some have modified VW and BMW units to get a better quality of stub axle. I suspect that they are more required for competition but not for street. Just a fun fact to know and tell...
Another fun fact is that I'm am led to understand is that bearing life was a problem with the S1 and S2 but that it was supposed to be fixed or at least greatly improved on the TC. That's what I understand and I'm praying it's true!