Hi Bulotavic. Nice to see you here!
As you probably know from 18watt.com, Richie Hall published the 18W TMB design in a rough and ready form that others could experiment with and tweak to their own tastes. Trinity's TMB is closer to Richies' original TMB design than the other two, although it is tweaked.
1 - The large cathode cap was in the original TMB. Personally I prefer not to use anything bigger than 1uF or possibly 2uF in that position.
2 - The Trinity Plexi deliberately uses cap and resistor values based on common Marshall Plexi preamp values. The Normal channel preamp is similar to a Plexi's dark/bass channel, for Plexi-style use with a patch cable between the two channels.
3 - The 100k resistor to ground reduces preamp gain, for later breakup. With the sIII the idea was to give more of a JTM45ish feel as far as breakup goes. The 470k mixer in the TMB is from a typical Plexi preamp.
4 - Yes, in a subtle way. I would also never refer to that pot as a Master Volume, since it only controls one of the two channels. It's really just a Volume control for the TMB channel.
5 - That is correct. The large cathode cap reduces more gain ,when non-bypassed. The Boost then switches a bypass cap and or parallel resistor across the cathode resistor.
I also really recommend taking a look at Unimind's Brown Plexi variant described in some recent threads, which sounds totally killer!