Thanks for the replies everyone ... <img src="/forums/images/graemlins/kewl.gif" alt="" />

I posted this on another forum as well, and got a good reply there as well. Here is the link - Thread over on YotaTech
And as Rusty said, for the lazy ...

"Hello,

I believe I made that post. you're going to have a few issues with using an automatic ECU and a manual tranny. First and foremost, the ECU is designed to communicate with the transmission- it takes inputs from the transmission and adjusts the ignition timing, and idle speed based on automatic specific inputs. It also controls the torque converter lockup, overdrive engagement, shift points, etc.. by analyzing throttle angle, speed sensor, and relative comparisons to an ASIC derived learning pattern. If you were to simply bolt in the motor and not attach an automatic transmission, you would end up with a CEL right off the bat, followed by strange idle conditions, and inherently poor overall performance. Your best bet would be to find a manual transmission ECU and engine wiring harness from the same year as your engine and get the sensors (MAF, A/F ratio, etc..) along with it. If this isn't possible, you need to find an ECU of a similar generation- meaning, if your injectors are the 99-02 style, get an ecu from that generation. If you're talking 95.5 to 98, get the electronics and sensors from that generation. There are different part numbers on the MAF and O2 / A/F sensors for almost every year but they will work within the same generation. 95.5 to 98 being one and 99-02 being the other. Another note, the engine harness from an auto can be used but the ECU connectors will be different between auto and manual. You will need to change some of the the plugs and the pinouts on some of the plugs, resulting in a large pain it the ass factor."

Look near the bottom of page one and into page two in the linked thread.

My reply to that was ...

"Unfortunatley, I kinda figured that my search for donor parts was far from over, I just wanted some confirmation. [email]D@mned[/email] integrated computers! (he,he,he)

Yes, the package that I located was from a '99 Runner, so we're talking about the more recent generation. I am not planning on adding the TRD S/C package, but having the upgraded electronics just in case would be nice.

This blows bigs chunks because I was offered a good deal on the package, $1500 for the package complete (including all accessories from a wrecked, but still intact Runner) pending exchange of my old 3.slo and corresponding parts. Not a bad deal if you ask me. Now it would appear that I will have to hit the pavement again, looking for components from a manual tranny vehicle. I will no doubt spend more money pulling the parts from multiple sources.

Switching gears slightly ... this '99 that I mentioned has an LCD odometer, hence I don't know the exact mileage on the Runner. The best guess of the yard owner was a range of 50-70,000 miles. I would like to know for sure before I drop the cash on it. I have no experience with LCD odometers. Would connecting a battery to the truck get that LCD working (along with the key of course)? I am not dead set on this particular donor, but it is mostly intact and a relatively recent wreck - I am not so sure about using a motor that's been sitting in his warehouse for years (not to mention the fact that those are bare naked engines).

Paul"

I hope this info helps you guys as well, and if anyone has info on that LCD odometer - thanks in advance.