Most important thing... Is it being sold with a RWC?
Out of the "CONS" you listed, the headunit and speakers missing is probably a good thing, it means you can personalise the stereo to whatever you want, and you're not paying for unnecessary items which you probably will change later on.
The boot carpet isn't such a big issue because there will probably be someone stripping their car and you should be able to find something on the forums.
Wheel Alignment should be done for RWC if I recall correctly, but putting new rims on shouldn't mean you need a wheel alignment, or do you mean wheel balancing?
You should be able to get the Aircon regassed for less than $200 so that shouldn't be an issue, but ask the current owner to do it in the condition of sale so you know that its working before you pick the car up.
The brakes you probably should get checked out, what kind of squeak is it? Does it sound like metal grinding on metal?
Whereabouts is the car? I'm sure someone on here that knows a lot about R32s would be more than happy to go check the car out for you
Also, any pics?