I have a very easy to follow PDF outlining the brake fluid bleed and replacement. PM me an email address if you want a copy.
In the 13 years I maintained my ST1300 I bled the brakes about 15 times (every 12,000 miles). I rode enough I never had to do it at 24 months. I also had a second ST1300 for a while that had very old brake fluid in it when I did major service on it at 70,000 miles. I always did this job by myself.
It was my experience that a MityVac works fine but needs help on some of the longer circuits. I would pump the foot pedal to help it pull fluid through. 8 or 12 pumps then check the reservoir. You only have to pull air into a circuit from the reservoir once to carefully pay attention from then on. The first time a Mityvac or other vacuum pump is used the trick is to wrap the bleeder valves with teflon tape to help seal the threads. You only have to seal them once, or at least once in 180,000 miles. I also replaced the end hose of the Mityvac with a piece of small ID vinyl hose that fit the bleeders very tightly and did not use the adapters supplied with the pump.
Yes, the proportioning control valve can be full of jelly-like material caused by neglected or incomplete flushing/bleeding. You are on to something there. It must be completely flushed out. There is a very specific sequence to bleeding each circuit and it must be followed. Besides the PDF I used and offer there are many resources to help you.