The trans problem is that the synchronizers ( especially second gear ) are gong out.. Find a used trasnny (about $350 to $500) from the pick and pull that has low as you can get miles on it..It will be cheaper than the rebuild. But if you want a rebuild then go for it,, about $700 to $1000 is normal around here..
Ah the brakes.. hmm sounds like you have enought of a caliper problem that you may be getting air into the system.. If I were going to replace all the parts that you mentioned then I would put out the little extra money and get the master cylinder...Even replacing the rubber hoses on the calipers and rear brakes are a must as they will deteriorate from the inside out..They come apart inside and make a type of one way valve that will cause back pressure in the system..