The brake issue sounds like air in the system, your dad is correct.
Brake Bleeding -Purging air and moisture from your brakes
There is a "generic" procedure for bleading brakes.. You may have to go to page three or four in the link to find the actual procedure. It also gives you a TON of information on bleeding brakes..
and for the transmission, here is an Ebay listing. It's a start.
eBay Motors: 1995 Ford Probe GT/MX-6 LS 2.5 V6 manual transmission (item 120298208371 end time Sep-23-08 20:26:48 PDT)
It may also help to know that the transmissions on the Ford Probe are the same transmissions found on the Mazda 626 and MX-6.
Be careful when buying one online thought... Make sure it is EXACTLY what your looking for.