It's fairly simpleHere's what you need (in order of importance)
1. Your thinking cap
2. a print out of the ratios. (if it's a hydro b-series trans, print out the ratios for the hydro b-series, LS, GSR, ITR, whatever)
3. a clutch (can be new or used, doesn't matter)
4. a screwdriver
A marker/paint pen will help.
1. Put trans in 3rd gear or 4th gear. if you put a screw driver or some sort of rod in the hole on the shift rod, push it forward and pull it back a few times. If you push the shift rod into the trans, 4th gear. If you pull it away from the trans, 3rd gear.
Now lets use some simple math. Pull out your cell phone, (or calculator if you're stuck in the 90's 
)
now lets see here, unknown civic hydro trans s20 (a000 stamp) shady buyer says it's a lx trans
LX ratios
3rd gear is 1.172
4th gear is 0.909
final = 4.058
3rd gear * final drive
1.172 * 4.058 = 4.755976
4th gear * final drive
0.909 * 4.058 = 3.688722
mark the differential, push shift rod in, engaging it in 4th gear. Put clutch on input shaft. Count how many clutch rotations it takes to make one full differential rotation.
It should be, 3.68 rotations. Since it's hard to count 0.68 of a rotation. Multiply 0.68 * 12. You'll get 8.16 So that means..... 3 rotations, and it will now be pointed in the 8 o'clock position.
However when you do this, you realize that it only takes 2.77225 rotations. So you bust out your table and you're like wtf, 2.77 rotations, what's that? so you multiply 4th gear by the final drive of every trans. There ya go, vx trans with 4th gear of 0.853 and final drive of 3.25
You just saved yourself from buying a transmission that has a 4th gear that lasts forever 
Tips:
Always check 3rd and 4th gears, here's why
cable si trans 4th gear
0.937 * 4.25 = 3.98225
cable zc trans 4th gear
1.033 * 3.88 = 4.0174704
Both 4th gears on the zc and the si trans have nearly the same ratio. So they would appear to be the same trans using this method. Lets try using 3rd gear
cable si trans 3rd gear
1.259 * 4.25 = 5.35075 (5 full 12 hour rotations, then landing just past 4 o' clock)
cable zc trans 3rd gear
1.346 * 3.88 = 5.2343248 (5 full 12 hour rotations, then landing just before 3 o' clock)
Mark the trans at your 12 o' clock position
