1) Better to start doing it late than never. If your three-way valve is still working at this point, you're probably OK.
2) It's safe to backflush any machine with a three-way valve. In fact, it should be mandatory, otherwise the vavle will eventually clog and fail. Not sure why manufacturers sometimes recommend against it, other than a general mistrust of the intelligence of their customers.
3) I don't think there's a real advantage to using a blind filter rather than a disc. Just whatever happens to be more convenient to you.
4) Check out Randy's website, espressomyespresso.com. He has a good tutorial on backflushing there.
http://espressomyespresso.com/However, the basic process is very simple. Insert blind filter or disc into PF. Place a small scoop of backflush detergent into the filter. Lock in. Pull a blank shot. When the machine comes to full pressure, turn off the brew button. The detergent should purge into the drip tray through the three-way valve. Repeat the process four or five times. Now rinse the detergent out of the blind filter and repeat the backflush procedure with water only for another five times. That's about it. Oh, and most people recommend pulling a "garbage shot" after you're done, to season the group and get rid of any excess detergent.