Brent has some good posts on this. Search on clutch, not transmission.
The main things I learned in no important order are:
1) Pull the pushrod from the slave cylinder before you pull the tranny.
2) Try to tape the right side of the tranny case to prevent scratches.
3) You need to raise the frame from the engine/tranny to get at the two starter screws (but no need to remove radiators or injectors).
4) The book shows three starter wires. My bike has two of these joined to one ring, so only two leads to the starter.
5) If you loosen the front engine bolts to allow it to drop easier, do not loosen too much, there is a loose nut buried behind the radiators, and you want to be able to retorque them without getting at the nut.
6) Get sorted out how you will support the two frame plates and the engine/tranny combo before you start. I used hydraulic jacks and a car scissors jack.
7) I liked Brent's idea of the 2x4 under the tranny on a jack. Makes it easy to handle if working alone.
8) When replacing the tranny, raise the frame enough to clear tranny mount and starter mount, but then lower the frame some to clear the right side tranny flat in the center. The frame curves in at the bottom, and prevents straight line up if the frame is to too high for the last inch or so that you have to push the tranny in.
On the seals, most comments say replace three, the tranny input shaft seal (clutch side), the slave seal and the tranny output shaft, both on the back. I replaced the indicator seal too, but I've never seen this mentioned. The only other one is for the shifter, and you can get at this one while the tranny is in place if needed. Note that some say not to replace seals that aren't leaking, which seems a bit superstitious to me, but I can imagine there is some merit in this thinking.
There seem to be old and new pushrods on the market. The new ones have a notch and a feltring that goes in the notch.
97 Bakker Dakar K1200RS