Rebuild it yourself. Rebuild kits can be had for fairly cheap, and they include bearings, synchros, synchro sleeves, etc. most of the big things you'll want to replace while you have your tranny apart. Here:
BSK-SYN101 Type R GSR B16 Bearing Seal and Carbon Synchro KIt - Synchrotech Transmissions Inc
What exactly do you need to know about the mainshaft and the counter shaft? It's ridiculously easy. The main shaft is the shaft that has the input on the end of it. The countershaft is the only other shaft in the transmission. 1st and 2nd are going to be your two larger gears, 3, 4, and 5 progressively get smaller. Check the teeth on the gear cones to be sure that there isn't any horrible amount of marring on the teeth of the gears. If your car won't go into gear at all, I suspect that the synchro sleeves are so badly warn that it simply won't allow for a gear change. It's either that or the teeth on the gear cone are so badly worn that it won't allow the sleeve to slide on the end of it. Chances are you'll get it apart and figure out that you need a 1-2 synchro sleeve and possibly to replace some of the gears themselves (not cheap).
You can figure out how to disassemble it from the thread linked above. When re-assembling, be SURE that everything is clean. Clean the magnet, clean the mating surface of both sides of the case, and any debris or shavings that may be in the gears or still inside the transmission. Also, you'll want to use a piece of 300-400 grit sandpaper to scuff the contact surface for the synchro on the gears themselves.
The contact surface is at the top of the gear in this picture. The teeth next to it are the ones you need to inspect for significant wear. The one in this pic appears to be badly worn. If the teeth still have their same general shape, you can just take a file and file down any points or disfigurations in the teeth. The teeth at the very bottom are the teeth that actually make contact when the car is in gear. Inspect those for wear as well. If there's any dings/dents in them you're going to want to replace the whole gear.
Let me know if you have any other questions, I have done 2 rebuilds in the past 6 months. One B16 hydro and one d16 hydro. Both turned out great.
OH and one last tip for disassembly. When you are pulling gears off the end of the shaft, set them all face down and put them in order. That way you can just pick them up and place them back on the shaft in the correct order