Sounds interesting - some pics would be nice. My personal opinion is to keep them as stock as possible, though I do appreciate the more wilder tuned cars out there. Handling isn't great so I'd recommend at least a lower front brace from PPP which are about £40 posted on ebay & a bolt on job.
Some Gs had electric windows from the factory, not many though I believe. It should be obvious as the switch gear etc. should look factory, though they could have been retro fitted factory items of course. Things like sunroofs, headlight washers, electric windows & fog lights were options - essentially part of what made the G40 uncompetitive with the Golf as the price racked up when 'speccing' a G to MK2 Golf GTI base spec.
The pulley & chip should take you to about 130bhp as the supercharger spins up faster producing more boost due to the smaller (68 or 65mm) pulley. The chip causes the ECU to retard the ignition & increase fuelling to keep the mixture as close to optimum (Stoichiometric) as possible to prevent detonation (lean conditions with too much Oxygen) which will lead to pistons melting, valves burning out & heads cracking.
I'd be looking at getting the supercharger rebuilt as a matter of course, PeteG40 on here is the man to talk to about that, if it goes bang it will be a massive problem. It may be worth having a look on the charger for any serial numbers scribed on from Jabbasport, then you can contact them for any potential service info. If it has been done recently then you may just get away with changing the internal drive/timing belt. Service interval on a stock charger is around 40,000 miles & with a chip & pulley I'd be looking at 20,000 miles.
I'd also have the injectors cleaned & tested as if one of these goes lean then you will also have a problem, I believe YOOF on here is the go-to man for that. You may also consider an Ali radiator, I did as my temps got a little bit 'twitchy' in Sheffield's rush-hour traffic, the Ali radiator sorted this - they're around £120 if you shop about.
The rest of the mechanics are essentially simple Polo mechanics & things like the cam belt & water pump, oil & oil filter, air filter & plugs/rotor arm/dizzy cap/leads should all be cheap (plugs aside) & easily available. I use Euro Car Parts & VW Trade Parts Services for Quantum Synta Oil & genuine filters. I'd be budgeting around a £700 - £1000 all in with the charger rebuild, though you may get change. A Haynes manual will be very useful & these are easily available.
As for missing bits like handles & seat belts etc. there are loads on ebay. Search 'Polo2F', 'MK3 Polo' or 'Polo G40' for bits-a-plenty, though some stuff is getting difficult to get, for example the 'PoloG40' rear badge & the 'Supercharged' script. Expect to pay more for certain G40 specific parts too, such as rocker gaskets. Again, I think PeteG40 on here keeps or can get some of the parts you might need.
Getting the handle open might require some force with a screwdriver. I have some odds & sods of handles & keys etc. I can sell you cheap to help you out if need be. If you're having the car painted anyway then I wouldn't worry too much.
Hope that helps. They're great cars which are very rare now & really get under your skin, as a recent new owner my self I'll be very interested with you're progress. I keep updating my 'build' thread but my car was a fairly well known car so was well looked after for a lot of it's life. I bought it after a slight downward ebb of ownership & spent a fair bit of time & money putting things right.
You've probably seen it but here's my thread, it's probably a little trivial at the side of some but hey ho.
https://www.polog40.co.uk/forum/index.php/topic,12642.0.htmlGill