I would think a viable route (if there is such a thing for this sort of project) would be to buy a NA aerotop for around £7-8K and a 6 speed TT for around £9-11K.
then strip the auto NA and do the necessary transmission tunnel mod's that i think i've heard are necessary (get it resprayed) and then transfer all the TT internals across and then sell the spare TT chassis and auto NA bits.
If you had a manual TT already, and could do alot of the general mechanics yourself, i reckon you could end up with a Royal sapphire pearl, 6 speed TT aerotop for a net outlay of approx £12K, or standard base colour with no leather for sub £10K.
£8K - NA aero
£5K - Towards adj to aero chassis and transfers of TT to aero shell (assumes alot of DIY)
£3K respray + cream leather retrimmed seats
with maybe £4K of bits left to sell.
This is all just pure speculation and could be miles out. I have no idea about the issues of if, for example, the NA wiring is adequate for all the TT functions or any of the numerous other problems of which i'm ignorant. It just seems to me that if you have both types of car then your parts problems are sorted it is 'only' a matter then of swapping the relevant bits.
BTW I think all of you auto to manual conversion wannabe's are mad, but would love to see one made.