Wow, I don't know where you are on this. I'm really sorry for being gone for so long. I've had some pretty hairy stuff going on for a while and wasn't really online. If you're still messing with this unit, I'll give you my IM and we can chat online. The truth is, I'm relatively out of touch with the whole thing as it's been a while. But let me give you a couple small pointers:
On the fans, I believe I have it set to "0" for the triggered value because the output is inverting (it uses the middle LED as the driver for the fans). You might change the Power On value to 1 so it doesn't briefly power them before you start.
The temp settings were always goofy - I think I list somewhere the numbers that I use. They aren't great, but no one has ever given me better. Basically, you just type the three numbers in I list and it gets the temps roughly correct in the range most people care about (~155-220f). It lets me set when the fans come on accurately, and that's fine.
FYI: The OEM water temp guage is crap. It lies to you. By the time the needle moves, it's generally too late. I linearlized mine some time ago, I don't know if I did a thread here on it, but I did take some pics to show what's involved:
Doing that will give you a handle on what's going on it other places. I guess you could just as well buy an aftermarket gauge - but basically the response is flat (needle not moving) for a 40-50 degree range.
With your idle valve being open, yes, it's very likely one of the two outputs you saw set to trigger on RPM. I have no idea why they are that way - I wonder if it's a change in the EXACT version of the MS-II code/.ini files. Unfortunately, the version of the code I did all my development on the MS guys decided to pretend never existed. They pulled it off all the servers and started numbering stuff out of order. At any rate, the output is overriding the idle code - so turn those off.
One of them is to control VICS (the one set for 5250), if you're still in this project and still stuck, let me know, I'll dig out the schematics and figure out which output is the one you need to tweak.
A couple quick questions: Is your wiring harness stock? You mentioned replacing it. Another friend had a similar problem with this set up - stuff wasn't working and it turned out his wiring wasn't stock.
Actually, let me see if you're still looking at this 6 months later. Again, sorry for not being around.