Here's a trick for the next time you need to stick the gearbox together.
Those teeth on the shifter quadrant...there are 5 of them. 5 speed transmission.
Bottom is first gear and so on. When you're putting the inner cover back on, line up the slot between tooth 1 and 2 with the centerline of the shifter shaft hole to index it. As long as you have the gearbox in neutral when you put it together, it slots right in.
Putting together and taking apart these 5 speeds is a piece of cake really. Just have to look at it and think about it a bit logically. The mainshaft gears are 5 to 1 from the inside out(big gears to smaller gears), the lay shaft is the opposite. The gears can only go on the shafts one way really, or it won't all fit in. The tricky part, which took me a few times putting in and taking it out, is figuring out which shifter fork went where and which order. But those can only go one direction if you look closely.
High gear mainshaft will already be in because it's holding the counter shaft sprocket. Next is the lay shaft with it's high gear on it. From there you just alternate gears with their forks one at a time. The indentations on the shifter cam plate are for each gear with neutral. Put the plate to neutral with the plunger and it will come to you. It's like putting a puzzle together.
Early 5 speed cam plates were round so you had to take high gear out to get the cam plate out. Later models had a flat area machined off so you turn it to remove it from the case without taking high gear out.
I've got A LOT of experience with this motor. Road race a '73 T140 with AHRMA and I have another TR7 for a street bike. I've rebuilt these motors many times. I love these bikes.
I prefer to break them in with either break in oil (Brad Penn SAE30 break in oil). Or at most auto parts stores in the motorcycle oils section you can find the Valvoline 20W-50 4 stk motorcycle oil. It doesn't have all the friction modifiers that regular motor oil usually has. Seems to work a treat as with the break in process, I can get my rings seated pretty quick.
The break in process is crucial with these because it's not all that easy to get the rings seated sometimes. Make sure you put the pistons in dry, no oil on the walls. I know a lot of people probably know that, but I've come across several that wanted to coat the walls down before sticking the pistons on.
After mine is broke in, I use 15-50 Mobil One synthetic. Never a problem. And that's coming from an engine that's been worked hard revving to 7500 for extended periods of time. I use 75-90 Mobil 1 synth in the gearbox as well.