First of all, what Andy says above seems about right to me.

You say that you want it fairly well spec'ed at the end, and you also say that you want something that has aftermarket parts readily available.

With the NSR's, the spec'ed up bits are the SE/SP bits: the dry clutch, the more adjustable suspension, and the lighter Magtek rims. Basically from there you start to delve into the HRC/F3 bits to up-spec it any more. As Andy says, you can generally get these bits used (and very rarely as new old stock) via Yahoo auctions Japan.

But what I would like to add is that to my way of thinking, the real fun to be had in trying to up-spec your machine has to do with the fact that it is a two-stroke. By this I mean that you can do some “tuning”. And to my mind, these are the “specs” that matter and make the bike your own.
Flow the crankcases, machine the heads to set the squish and combustion volume, get the Dremmel out and clean up any little casting daggs in the barrel ports etc.
In my case I have installed some Wossner RM125 pistons which are almost as light as the F3 pistons and bolted in a set of MotoTassinari V-Force 3 reed blocks. I, admittedly unknowingly, think that they will work really well with the flowing I did to the crankcases.
And, in the future I may try an aftermarket programmable ignition such as Zeeltronics or Ignitech for example. And then of course there is carburation and jetting. And the pipes.

I realise that playing about like this is not everyones “cup of tea” and will probably result in some serious problems and expense etc. But for me all the fun is in trying these things and you can often learn a lot along the way.

Myself, I like the challenge of trying to use modern equipment/ideas to get some grunt delivered down to the tarmac. Others are probably happy to stick in a few F3 parts. Some may like the idea of an original SP. Or alternatively you might like to try something along the lines of the TYGA 300cc kit.

Different people will be happy going about their restoration in their own different ways, and thats cool because it ends up being a bike that that particular owner couldn't be happier with.

So what I would say to someone looking to start an NSR restoration is to first figure out what sort of restoration you want to do, as this may have quite an influence on what is important in the bike you buy. And that is my 2 cents.