... Neither Paraglow was on until I cut the power off, then back on. ...
Sorry, I didn't follow that - it appears to indicate there was no LED glow when the amp was not powered, which does not seem like a problem ... I'm pretty sure you meant something different though! :^) So, how many switches are you using - there is the power switch on each amp, the speaker switch, and possibly a power strip the amps are plugged into (?).
Aside from that, sure you can replace a 2A3 with a 300B by just changing the filament voltage. It will perform pretty much the same (power, voltage, current, gain, etc.) except for probably 6dB more hum from the filaments. You will of course hear the intrinsic timbral differences, such as mechanical vibration of the internal parts and linearity, and probably some things we haven't identified yet.
I can't see how the unloaded secondary or the balanced power can be a problem.
I applaud your careful, exploratory approach!