#1
After looking at the numerous schematics and etc, I believe that the concept of Mesa Mark I is the most feasible one available for a Blues Junior Hot Rodding. The problem is that, aside from Santana's music, I have difficulty finding video/music samples of Mesa mark I on youtube.

Furthermore, I was wondering is there any things that makes Mark I special (in terms of Mesa), so much that they reissued Mark I even with Mesa Mark IV.

No, it won't be Mesa by a long shot, but it will likely to have a cascading quad gain stage like Mark I.
Ibanez SA-120 (ed.2006)
BluesJr 1996-B + cathode follower + texas Heat
Crate CPB150
Homemade 4 x 10 cab Bass closeback
Metal Muff
#2
Have you tried the Mesa forums? They could definitely help more than UG. They have some pretty knowledgeable people there.
#3
I assume you're going to completely remove the PCB, in which case the possibilities are nearly endless. Personally, I'd make it into an 18 watter, since the transformers can be reused.
#4
Instead of calling it a Mesa style hot rod, I would call it Mesa-inspired hot rodding, and probably just at the preamp section.
Ibanez SA-120 (ed.2006)
BluesJr 1996-B + cathode follower + texas Heat
Crate CPB150
Homemade 4 x 10 cab Bass closeback
Metal Muff