There is no way that is a 2.5k repair bill.. Lets look at it this way, the best way to approach this is to remove the engine from the car, so that the gearbox can also come out and everything is easy to work on. Open gearbox and replace worn synchros. While gearbox is apart replace bearings and seals. Separate head from block. Freshen up engine, this may require more than just rings and seals, it may need machining etc. Replace head bolts, gaskets, main seals. Inspect clutch, replace if necessary, machine flywheel, replace flywheel bolts. Replace water pump, thermostat, cam belt.
Now, engine is out so it would make sense to check things like engine mounts, replace any hard to reach items like oil pump.. If you are doing a job may as well do it properly.
Using OEM parts and gaskets and good quality fastenings like ARP it's gonna get expensive, especially if the head needs a bit of machining.
Then there is the cooling system, what's rusty? Coolant manifold? May need replaced. Along with the radiator.
Then the suspension, this won't be too expensive though. So yeah. Sorry but to do it properly will cost more than what you think.