Did you actually get any feedback on your car value, Andy?
I have been thinking about this even more the last few days as we're in a similar position, from what I recall you have some very good but removable mods (audio, exhaust, wheels etc) that would probably mean you get more, assuming you still have the old bits?
I see an awful lot of TDI's for sale from 53-55 plates in the £4xxx bracket. However most of them are dogs with high miles and extremely basic spec. Also, how many suffer from rusty wings now too?
I would think you'd get up to £6k for yours, but it all depends on mods whether you'd get more or less than that. The fact the mk7 is out soon won't help current/future values either. Have a good look an Autotrader, and get some valuations from Glass etc. I got one and it came in at a figure I had in my head already.
Was going to look at an 06 R32 but saw that these are also suffering badly from corroded wings - having already been through a claim with my car it's sort of putting me off another mk5