Robsteeler66
XS400 Addict
Looks good. Congrats on the new scoot!
I would do a full dissemble, not just a cleaning. You can leave the motor in if you want; it's easy enough to take out later if there is a problem.
Are you trying to stick with original replacement parts only? Aftermarket master cylinders are pretty cheap, even new. OEM will cost a lot more if it comes to that.
If you have access to an ultrasonic cleaner those brake parts should turn out pretty well.