1) Would you negotiate a deal on this truck, what would be a fair price to pay?
Depends. The motor is unknown condition. Could have 300k on it. It's partial and incomplete. <$500 is where I'd start.
2) Can I use a mass air flow and filter box from another 2/3RZ
Sure. You'll have to match the ignition type. Exactly which years are compatible, I'm not sure.
3) Will my transmission bolt up to the bell housing from the 2wd transmission
No. It appears that you need a 2TR (later model tacoma) bellhousing.
Read:
http://www.pirate4x4.com/forum/toyota-tacoma/682430-3rz-r151-single-twin-stick.html4) if the rear cat is missing, can I use a generic cat or does it have to be a Toyota cat.
Generics work fine. Size it appropriately.