Hi, welcome to the forum.
I think your rattly windows may be down to the seals being old and not fitting as flush as they once did. The wind gets in the edges of the glass and the buffetting causes the glass to rattle around a bit as it's no longer forming a relatively good seal. Once you've got new door & window seals you may notice a difference, which brings me nicely onto sourcing some of the parts you're after...
Ebay - it's you're best bet as some of the parts are obsolete from VW and have been for years. Search around and you'll find people breaking MK1 Cabs for spares and these are you best bet for seals etc. They do go for silly money though - be warned! If anyone knows where you can get seals new then please let me know as well. ÂÂÂ

Bootlids - ebay again.
Roof - depends on how much you want to spend. If it's the inner headlining that's ripped then you can either have a go at repairing it as I've been told these are nigh on impossible to replace without removing the outer roof skin first.
I've been quoted £150-£180 for a new inner hood lining, though others in the forum might be able to advise you on cheaper ones? I'm having a new mohair roof supplied and fitted for £425 which I didn't think was too bad ( ÂÂÂ

) but I know it can be done for less.
Your doors might have dropped on the hinges a bit. I'm sure it's easily fixed but not been mechanically gifted at all I'm best off leaving the others to advise you on that!
Hope this helps a little. In the meantime rest assurred you've got a classic and it'll be well worth the financial outlay in the long term, both in driver satisfaction and general kudos!
Phil