Clutch should be ok at Stage 1 but any further and you'll want to upgrade that. DSG by contrast doesn't need upgrading until you have more output than the K04 can do--i.e. only need to look into that if you upgrade the turbo. While I know you're probably dead set on the manual, I'll get to the reason I mention this at the end...
As for tunes I think the posts above have covered it though I will say if you're after a canned/OTS tune you can do at home yourself, I like IE for a few reasons. However at least one person has reported an IE tune not working on their Euro spec car (I don't think it was UK but another country), so something you'd want to confirm with them if you go that route.
Personally I think Stage 1 is a bit of a waste on the S. Obviously it's better than stock but I really think Stage 2 is the most ideal as you get the best bang for your buck IMO. The tunes are really not significantly more expensive (like $50-100 more for most OTS tunes between Stages 1 and 2) but Stage 2 gives a whole lot more performance. Yes you need to upgrade the HPFP and add a DP but, to me, it's all well worth it since you're more or less maximising what you can get out of the engine and stock turbo for less $$$ than all the other engine choices.
Only problem is going back to the top here--the clutch pedal car will probably need the clutch upgraded too which is additional cost you don't have on the DSG. People (and tuners) will tell you you "need" a tune on the DSG of course but IMO you don't need a tune at all; even if you go for a DSG tune, it's likely cheaper than P&L on a clutch upgrade. Again I think you're probably set on a clutch pedal car, and that's fine, but I'm just putting that out there to think about.
