First off Welcome

and nice to see another Breadvan! (i've recently brought one myself).
Your plans sound good, but first off i would sort these bits out with first priority:
- Sort your rust out
- Find some nice BIG tyres & alloys
- Slam it
Then focus on you're other bits such all the exterior styling
oh also, why are you thinking of putting a sub in the boot -
BELOW a set of 6x9s!!!?!?!??!?!
All 6x9s are are mini-subs basically and they draw a huge amount of air as they are by themselves, if you put a sub next to, or underneith those 6x9s your sub & amps will sound horribly out of place as they require a certain volume of air each, and having 6x9s & a sub in a small boot of a MKII squareback you're not going to have enough air to allow both sets of speakers to displace properly.
Personally on the audio side of things i would stick a reasonable headunit it (nothing amazing / or over £150) and put some 4+ gauge wires in - the more power that is being transmitted means more resistance, the larger the wires the larger the resistance = better quality.
If you want a really good audio setup i would do this:
- Leave the sub out as there are much better ways of gaining bass without destroying your EQ.
- Buy 2 component sets, i suggest some good quality:
-- Tweeters + 6.5" Midd-Bass - put these in your passenger side panels - and make sure they are as centered as possible (you'll get more air to them) - but make sure the tweeters are further back than the midd bass)
-- Tweeters + 4.5" Component Speakers - put the tweeters more to the front of the car.
Don't run cross overs, run an amp so you'll be using 6 channels instead of 4 plus 4 crossovers, then buy a headunit with good EQ settings and you'll have a bloody good sound system.
You have a PM with regards to some parts which i think u may need.. or want..
hope this helps
