I am re-reading all of the rules myself....original rulebook text and the warmuster #2 rulebook.
1.) There is no talk at all about the hits from shooting so I will need to use the default rules of shooting a unit and disregard all outstanding hits at the end of the shooting phase. Even the high elves could cast a 3 shooting attack spell that ignores armor and should be able to focus fire on the siege engine per the warmuster rules and take them out. Just never happened in my case, I tried.

2.) In all examples of an assault on walls using a siege tower, the troops are on the ground, behind the tower, and you are forced to IMAGINE the troops assaulting from it. I see a rule again and again about how "if the accompanying troops are ever forced to retreat from combat, the tower is destroyed". So, no matter how your towers are represented on the battle field, to scale and very useable like mine, they seem to not be physically used at all in the rulebook so I would have to say that if a unit uses a siege tower to assault a wall section and loses the assault, forced to retreat, then the siege tower must be destroyed. All of this makes me want much smaller siege towers and actually put them behind the infantry to clarify what you are shooting at and what you are charging against and to actually just imagine the fight on the wall.
3.) As for the tower. Towers are not mentioned very much at all in the original rules but have a lot of text in the warmuster e-zine. specifically, stands can assault from up to 3 facings at one time "but must be from different units". The three faces may be, in my case, the 2 attached wall sections and the courtyard. So then there would need to be 1 unit on each side of the tower and 1 unit in the courtyard to get 3 stands into combat with a stand of the tower defenders. From what I get from the text and the example rules text, you cannot just simply make your way through the tower to the other side. I would have been forced to assault the defenders of the tower. Once I wipe them out and capture the tower I could then use all three faces for my own movement and use it's doors to get to the other wall sections or courtyard.
I am not a master at this so these are my suggestions only, I could be wrong. Let me know what you think.
Thank you.