TeamShiftPoint is correct.. The OBDII port can easily be used by adding on the diagnostic plug. I found that you can install an OBDII plug right above the hood latch pull and it looks like it was installed from the factory. Also, your check engine lamp will work just fine. The 5VZFE ECU provides a ground path to illuminate the lamp just like your 3VZ ECU. Again, you need to be comfortable with crunching through the wiring diagrams as you'll be building this sh*t from scratch.

Regarding your question about the plugs- You will be harvesting the plugs referred to as IH1 & IH2 in the 91 4Runner EWD. They will contain the speed sensor, check engine light, 4wd indicator, back up lights, starter signal, batt & ignition power, O2 sensor, etc.. Don't even try this without the correct EWD's. If you need to purchase them, call the Toyota Material Distribution Center @ (800) 622-2033 and get the 91 4Runner EWD and the XXXX Tacoma, 4Runner or T100 EWD. (XXXX represents the year of the donor motor)

Another note for your swap- Toyota changed the 3.4 setup somewhat in the 99 model year. They ran larger injectors and ditched the cumbersome MAF used previously along with the EGR system. Also, the earlier models 95 & 96 Taco & T100 had an ECU that wasn't capable of supporting the supercharger. However, the 96 4Runner was capable of supporting the supercharger. But, in order to take advantage of all the cool upgrades they made, you would ideally find a 2000 - 2001 Tacoma or 1999 to 2000 4Runner. To my knowledge, these are the ones that ran the larger injectors, no EGR and no drive by wire throttle system. I would avoid the drive by wire system as it would represent an additional pain in the as$ to wire. This is a fairly technical wiring project, if you're not down with it so far, I would call Mike at Offroad Solutions and get a price from him.