mmc3 problems...

No. The only way to change the I flag in the 6502 is through opcodes like CLI/SEI/RTI/PLP (and I guess IRQ/NMI/Resets set the I flag -- but you know what I mean). These registers change the MMC3 IRQ enable flag (enabling/disabling MMC3 IRQ generation -- but not affecting the I flag on the 6502).



Well I still think copying mem everytime the game bankswaps is a bad idea -- it'd be so much easier to just change a pointer. But anyway...

Anyway:

At any time when $8000.6 is clear:
$8000 is swapped to page X
$C000 is swapped to 2nd last PRG page in the ROM

At any time when $8000.6 is set:
$8000 is swapped to 2nd last PRG page in the ROM
$C000 is swapped to page X

Where "page X" is the value last written to $8001 in mode 6



That is correct



Technically speaking, the IRQ counter decrements on every rising edge (0->1) of A12. Basically, under ideal conditions this happens once every rendered scanline on scanline cycle 260. When the IRQ counter becomes 0, an IRQ is fired. Kevtris doc covers other details quite well.

Every time there's a rising edge (again, basically this happens once a scanline -- but it can happen under other conditions as well):

if IRQ counter is 0, reload IRQ counter with reload value
else
{
decrement IRQ counter
if IRQ counter just became 0 and if MMC3 IRQs are enabled, raise 'IRQ pending' flag
}

if the IRQ pending flag is raised, IRQ are being fired nonstop until the flag is lowered (it is lowered with the IRQ is acknowledged -- as kevtris' doc puts it). Of course, IRQs fired by the MMC3 are ignored if the I flag is set -- but as soon as the I flag is cleared... you fire an IRQ if requested.

There is no way for the game to directly set the IRQ counter -- closest thing it can do is clear the IRQ counter by writing to $C001


EDIT:

Just realized I had my swap modes backwards -- whoopsie! Hopefully I didn't screw you up too much. Anyway I fixed them with this edit. $8000.6 clear makes $8000 swappable! Not the other way around.