Hey, fermin
#2 - The u-joint boot is always a PITA. I replaced a torn boot on my 1981 R65 but do not recall the "notch" you mention as I've slept since then. If the boot is installed in such a way that any lubricant reservoir can be exposed to the ambient atmosphere, then yes, you may likely continue to stain the driveway.
Perhaps a photo may show up... Guys?
#3 - The shifter shaft seal is installed from the exterior. When the shaft is removed, the trans oil begins to run out. Suggest you lean the bike over against a sturdy, padded support before beginning the work. Not knowing the year of your bike but my 81 and 83 R65s use a 26X16X7 seal. Confirm your needs. Dot not set the seal any deeper than flush with the outside of the case. A t-i-n-y bit recessed would be OK.
#4 - Use the correct crush washer to prevent leaks and do not over tighten the bolt. Just torque it down until you feel the threads strip, then back off a quarter turn.

Monte