With regards to the input jack, EMG's require a stereo input jack because one lug is wired to the negative terminal of the battery (if memory serves me correct....). Alot of guitars only come with a mono input jack because a guitar with passive pickups only needs a mono input jack. But Ibanez guitars come with a stereo input jack stock, so it saves you the hassle of replacing it (I think that the EMG jacks won't even fit in an Ibanez or something?). As far as the electronics go, I would advise againt wiring up a guitar with part active/part passive wiring. The ONLY way to get around this would be to use one of EMG's active preamp boosters on the passives to convert them to low impedance, high output like the EMG 81. This is a big hassle, and I think that you would be better of either:
A. Wiring up the 81 as 1 vol. 1 tone, and not wiring the rest of the passive electronics up. (1 bridge EMG81, 1 vol., 1 tone)
B. Getting an EMG 85 or 89 to put in the neck, a single coil EMG for the middle. This would be fully active electronis and although more expensive than just the 81, it would save you a headache and look better IMO. If you have the dough, opt for this.
No matter what you do, I think that the actual wiring will not be too difficult of you take your time and follow the diagrams. Go poke around here
and look at the diagrams to get a good understanding of what you are up against. If all else fails, shell out an extra $20-30 and have an experienced tech wire it up for you. In the end it sounds like you are after the EMG sound, and I think that after all the work of rewiring a guitar you will be very pleased with the results.