Hi mate
Well from talking to people who have the money to buy a Minker & have offered me money for my car in the past I would say:
Interior mods are of little concern. Minker's where basically bogo interior's anyway unless something else was ordered.
As long as it's done nice & suits the car it's not going to drop it's value.
Keep the flocked part's thou either store or keep fitted.
Body wise is tricky as most people would like to see the car as almost STD looking if a 323
Engine wise a fair bit can be done that won't make it look any different that will give it more go.
Yours already has had some bits messed with.
Engine needs to look as TT intended.
Air filter tops Alan did have as he gave me some, also I think I know where some are in a garage.
What I would say is mod the gearbox as I have done.
The petrol savings are worth it alone & alot of people think Minker's had a better 5th anyway
I would agree that the wheels are a night mare & need to be replaced.
Must be set of 5.
People for some reason remember they had Bottger alloys so really you need to source some.
But TT would have fitted any alloy you asked for but people think Bottger is a must.
Bottger 7 spoke 7Jx15H2 ET26 was what the press 323 had, ultra rare & will be almost impossible to get.
I do know where the spare alloy of the old press car is thou if needed.
Bottger 9 spoke 7Jx15H2 ET26 where fitted to loads of TT cars including the Minkers. Mine has them, press K1 has them with a fancy paint job.
Very good chance of getting these mate.

Ford Motorsport 7 spoke 7JX15H2 ET28 where fitted to the last few TT Sierra's as TT couldn't get the Bottger 7 spoke anymore.
Look almost the same as the Bottger 323 wheels. Good chance of finding these too & is a TT fitted alloy.
I have a set for track use.

To sum up it's your car so do what you want but if you want to recover your investment do it in a way that the car can be restored to as TT intended.
That's what I have done with mine.
Goodluck