From what I understand, the five port setup is for timing reasons. Each controller status is read in sequence, and the software interprets the controllers in said sequential order. This was correlated by certain older software exhibiting strange behavior when the multitap was used (such as two controllers working for single player games but only certain switches on one and certain others on the second actually having any effect). Back then, software designers (even Hudson's own staff) were not 100% familiar with how the controller port was timed, so errors like that appeared with the multitap. But they got the hang of it eventually, and by the time the PCE made it to US shores, only one game (China Warrior) suffered from the problem (since the only change to this 1987 game was the title screen). Having only 4 ports would also have been a marketing disadvantage, since the NES had a four-player option and NEC wanted to beat Nintendo in any way possible (Hudson didn't care either way; after all, they were Nintendo's first third-party).
In any event, have you made any progress with the conversion? I've had no free time so nothing's happened over here, heh.

Having a new baby in the house tends to suck up any notion of "free time".