Yes, you can swap between tunes like changing a Smarty tune, but it's all pre-loaded so you just pick your desired tune from the menu and download it to the car. Not sure how many tunes the loader holds, but I have 3 on mine.
I got my clutch from Boraparts. It's a Der Chimera Stage II. A little stiffer on the pedal effort compared to stock, but you get used to it. My 110 lb girlfriend drives it without a problem.
If you plan on any higher HP, I would stay away from the automatics. Even stock they seemed to have trouble going past 100k miles. A clutch is pretty easy to change, you need a way to support the engine from the top while having a floor jack beneath it to drop the trans down. Some people do it with an engine hoist up top, others with a 4x4 and ratchet straps across the shock towers (or a purpose-built shock tower support like you can get from Harbor Freight). You will need a few specialized tools (triple-square drive bits). IIRC it took me about 8 hours total between 2 evenings, taking my time and frequently coming in the house to warm up (it was in the middle of winter). I posted on tdiclub.com forum (username MichaelP) with some tips after I did mine, just search for posts under my name.