The `99 gearset I used came already installed on the trapdoor, however, it was from a bagger and my bike is a softail. I had to remove the gearshafts from the trapdoor so I could drill it for a drain plug.
Older softails did not have a drain plug in the bottom of the tranny case, they drain from a plug in the trapdoor.
I could have put the new gearset onto my old trap door, but the `99 uses larger bearings in the trapdoor and I liked the idea of the bigger bearings.
One thing to make sure you do is to use all the same year stuff, don`t mix and match gears from different years, there have been changes made along the way.
If you get a gearset with low mileage your trapdoor bearings should be ok.
You should replace the big ball bearing on the left side of the transmission case, also the needle bearing on the left side of the case that supports the countershaft.
You will probably be replacing the main drive gear, it will come with the gearset (hopefully). Suggest new needle bearings (2) in the main drive gear.
My clutch cable goes into the clutch mechanism cover on the lower front of the cover.
Have you decided what you are going to do as far as the clutch is concerned?