Thank you 5twins and wxjmx.
Thanks for reminding me to polish the seal contact area on the shafts. I always do that with the push rod, but I might have forgotten with the output and crank shafts.
wxjmx, good info, and interesting video. I have never seen anyone hammer a seal puller into a seal like in that video before. I guess the full 25 minute video would be good for someone who has never repaired anything at all before. Otherwise, skip the first 15 minutes, watch the next 4 minutes, and skip the last 6 minutes.
Couple more things:
Green Scotch-Brite pads are pretty aggressive, but 3M doesn't tell you how aggressive, and there are lots of imitators out there, so you really never know what you are getting.
I prefer to buy Scotch-Brite pads on this chart, by the box, but you can buy single pads at Home Depot. My favorite is White 7445. It WILL NOT scratch anything, not even aluminum, brass or paint. They hold an incredible amount of dirt, and can be rinsed and reused repeatedly.
Next favorite is Light Gray 7448, but it WILL leave fine scratch marks on aluminum and paint.
Finally, I use Maroon or Brown, but I don't use these much.
So, from less to more aggressive, I am using flint, silicon carbide, and aluminum oxide. 3M will not even tell you what the abrasive is in a green Scotch-Brite.
Personally, I think a green Scotch-Brite is a bit aggresive for shaft polishing.
Second thing:
There seems to be differing opinions on whether or not to use sealant on seals. My belief is that it is incorrect to use sealant on seals. Hans J. Pahl does not use sealant on seals in the translated German manual. I don't think any of the other XS650 manuals ever mention using sealant on seals either. I think sealant makes subsequent disassembly more difficult, and adds to the clean-up before reassembly is possible. In my opinion, it is especially unnecessary on seals that are placed, not pushed into position. That would be the push rod, output shaft, and crank seals on split cases. When you are pushing seals in, I think an appropriate lubricant is helpful, but sticky substances, such as Yamabond, et al, are counterproductive, and just get wiped off as the seal pushes in anyway. The lubricant I like to use is:
http://www.itwconsumer.com/userfiles/files/techdata-sheet/VC Tech Data/34000 TDS.pdf
It starts out slippery, then becomes a non-drying, flexible sealant. I also use it on gaskets, depending on the situation, and I especially use it on gaskets with minor tears. I think this is a very similar product to Gasgacinch.
However... I do wonder if the same motor oil that the seal is sealing against might be a better lubricant. Prime Seal contains ethanol, propanol, and methyl isobutyl ketone, and who knows what effect they have on seals. Yamabond also has weird chemicals in it.
Opposing opinions encouraged.