I only have an insight on the first of your three questions but I am sure that someone, maybe @gunrunnerjohn, will answer the others - especially whether this particular smoke unit can be upgraded with his SuperChuffer.
I do recognize the "[semi-]smart" smoke unit for this engine from the Lionel replacement parts pages. But this might be a substitute for the original stock smoke unit given that your engine dates from 2004 - does yours have a fibre sleeve on the resistor or instead does it look like this PCB and complete unit?
On the assumption that it does/this is the original equipment, these units originally came with a 6 Ohm resistor that was prone to overtax the AC regulator and the spec was later changed to 8 Ohm. More importantly, these are later models than the Lionel smoke units featured in what I think was Mike Reagan's "Smoke Unit 101" video about tuning up units that had fibre sleeves on 22 Ohm resistors by removing the sleeve and enlarging the air inlet hole above the impeller.
In any case I'd be very cautious about trying to enlarge the hole on your unit because (a) there are circuit traces near it you might accidentally cut and (b) these particular smoke unit PCBs are no longer available from Lionel so not easy to replace. In my experience they smoked like the Dickens right out of the box and maybe the best you can do is replace the wadding, although I'll be corrected about that if someone more expert has another idea.
I have not heard the pulsing noise you mention but then the engines I have with this particular smoke unit are very early Legacy and not TMCC.