Thomas,
You've got it right.
Press the shaft onto the rotary seal using the rotary seal tool.
Press the shaft with the rotary seal installed into the housing and through the gear using the tool.
The rotary seal is a one piece unit and MUST be installed with the tool. The reason is that the inner and outer part of the seal are connected with a rubberized fabric diaphragm inside. When being installed the inner and outer parts of the seal must move together at a specified distance from each other or the inner diaphragm will be destroyed. The tool insures that this critical distance is maintained while the seal is being installed.
Pressing the shaft back out may or may not be necessary. If you do have to press it back, it will only be a fraction of a mm. Just enough to align the washer with the housing. Be sure to drill the right size hole in the flat metal plate. The hole (I don't remember the size but it's in the heavy maintenance manual) should be just big enough to accept the shaft. When you place the shaft in the plate hole, the rotary seal will come to rest against the plate. When you press the shaft back with the bolt, you are actually pushing the shaft back through the inner portion of the rotary seal. BE VERY CAREFUL if you have to press the shaft back out. If you go too far out, you cannot press it back in and will have to start over with a new rotary seal. The rotary seals cannot be removed without destroying them.
I don't know if I'm doing a very good job of describing this job. If anyone else can help, please do.
Bill.