I really wouldn't worry about the brakes Brad, it's a 3000 pound load, not a 40' toy hauler. Your truck will stop it just fine, drive it in tow/haul mode and you'll be a lot happier.
Before you get all the new parts on it, try putting some fluid in the old master cylinder and see if it has a line that is leaking. While DOT 3 draws water like a sponge it usually doesn't just evaporate. If the master is empty then you most likely have a leak somewhere. Check it with the old stuff so you'll know if you need new lines. Lots of camper repair places still sell all the parts for those brake systems.
Brad, do yourself a favor, cut that hunk of sh*t off the 3" tube and get the entire new actuator. I tried to "restore" my old Trailrite with that exact actuator set-up that did exactly what yours is doing, and trust me, the headaches you will avoid will offset the additional cost. Drill the 4 holes and It will bolt back onto the tube, or weld the new one on. Also forget trying to flush the old lines, get the flex hose kit. It is so easy to install. If your master cylinder looks that bad, the lines will be worse...or like Skip said, you could just weld a new hitch onto the 3" tube and forget the brakes.
p-jet
after pricing out the parts and weighing in the hassle, youre right....i can get a complete one for about $140
http://shop.easternmarine.com/index.cfm?fuseaction=catalog.prodInfo&productID=4427&categoryID=150
I am unable to find a flex hose kit....everything ive seen is hardline kits....post up a link of what you are talkin about. thanks!