With the availability of manual 2.0 Gti's it really would be the most simple way to go about it...
I've not done the conversion, but I imagine the easiest way to do it is going to be to buy a manual car and rob it of all the necessary bits. Like you've said, you will need a pedal box and gear linkage [presume you will be going 020 like factory 8v Gti's, but you could go 02A if you wanted .. obviously this will change the pedal box and linkage requirements..), plus a gearbox/flywhee/clutch plus clutch cable (or hydraulic pipes depending on conversion), speedo cable? gearbox mounts and brackets? Don't know if there's any wiring involved for the Auto 'box? Guess that'll need removing.
Actually yeah, seeing as you'll have to buy a manual car for all the bits, probably best just buying a good one and driving it. Not trying to discourage, but you are just creating work for yourself. Only reason I would do it is for a full engine change, but if going 16v or VR6 I'd just buy one of those in the first place, so unless you're going to stick a 20v in it, it doesn't seem worth the effort.