do we want to include any of these?
Well, it basically depends on how complicated the changes are. I'd want to hold off on anything overly invasive for now. Here's my estimates.
# Lower the Flagpole Height
This might be as simple as changing a few constants. However, there is the issue of points. Depending on how the flagpole points routine works, making everything work correctly (i.e. proper values at the top and bottom) could get complicated.
# Lower bowser bridge, rope and axe
Should be pretty simple. All it proabably requires is changing a few constants.
# Modify Bowser behavior to match SMBS more (doesn't jump as high, moves faster)
This really depends on bowser's AI routines (which, as I recall are kinda involved). It could be as simple as tweaking a few values, in which case I'd say go for it. Or it could involve substantial editing, in which case I'd say hold off.
# Modify game clock timer
This is solved, I just need to add the value you derived into the code base. I'll do it next time dig into the code. (Should be soon, perhaps tomorrow if I have some free time.)
# Fix 4-3 vine issue
This needs some research done. I've never really investigated the vine routines, so I don't know what exactly it will entail. However, as a bug, rather than a new feature, it's gotta be taken care of.
I'll look into all of these and give you some more definite answers. All of your suggestions are things that should ultimately be done, but when depends on the size of the changes. I'll incorporate the game clock change and see what I can do about the vine bug. Once those are done I'll look into the other changes you've suggested.
Good night and keep upt the good work. Hopefully I'll release another patch soon.