If you're going with a TDI-M and not using the VNT15, you won't have mount issues. Just use the exhaust manifold from a 1.6TD or a 1.9TD along with the turbo setup and you're golden.
For the 02J tranny, if you're getting it, you'll have to go with the hydraulic clutch conversion. If you go with the cable conversion from an 02A/C on the 02J, the reverse light sensor gets in the way of the bracket. If you go with hydraulic, you'll need the pedal cluster, clutch master/slave, firewall bracket, hose, and brake fluid reservoir.
For the 02A or 02J, you can use the 02A/02C transmission console and bracket. I have them running on the 02J that I'm swapping in.
the only other concern is that you'll have to clearance the frame rail just like the VR6 swaps. Look at my sig for more on that. You'll also have to clock the oil cooler and use longer hoses to reach around as the 020/02A front mount interferes with the routing of that.
If you do go with a hydraulic clutch, you can easily go with the cable shift as well. It's not that hard and you can mount it in the stock height. Here's what I did with mine.
http://www.vwfixx.com/forums/index.php?showtopic=47349&st=225I wouldn't worry too much if the passenger's rear ear was broken. You won't use the MKIV mounts on an M-TDI. You don't even need to do it on a full as-is TDI swap. Just cutout some of your rear mount. You do want to check to see if the tranny mount snapped as that's where you would mount your 02A/02C console and mount.
Check to see what kind of damage might have been done to the transfer case and CV's.
...and your 02A will bolt right in there and can even use the cable clutch.