Test the mercathode system on a trailer boat without shore power? Really?
The Mercathode system is a 12V item, not a 120V item. While not ideal, you can test it out of the water to at least see if it's "supposedly" doing it's thing - the controller, anyways.
"Timing props"... this is one of those long-time myths. However, there is some truth to it - but the truth centers around the old, Mercruiser Blackhawk drives. Those needed to have their props timed or the two props would pound water into the anti-ventilation plate. Every once in a great, great, GREAT while you hear about how timing the props on a B3 took care of a vibration issue... but it's pretty rare. NOW, even knowing all this... I still time 'em!
Your original anodes (assuming either Mg or Al) where just fine. You didn't need to throw them away - they had plenty of life left in them - plenty (from what I could see in the pic, anyways). The new ones will not work any better than the old ones. Did you check around with local, experienced, boaters (with B3's) to see if Mg is the better anode for your particular waters? Often times, Al works better.
Brass/steel brush... the reason I mentioned it was that a steel brush will sometimes leave traces of itself in the SS - not always something you can feel. This can lead to rust spotting. Not the end of the world, though. Although any left in the Al of the drive can hasten galvanic corrosion - but it will be minor.