I believe the 2500 is worlds above the MS ... There are
tons of tuning capabilities in there, not the least of which is the long-term trim learning. Check out the Haltech videos.
I have an Elite 2500, Wideband Controller and Expansion box sitting on the shelf waiting for warmer weather in a couple of months for '94TT. Was originally going to be for the stock twins while moving to a VVTi head, but I think I'm going to switch to single with an FSR Street Fighter kit
What are your aims with the wiring harness ? Why not use the existing stock one ? In my case I'll be using the stock harness, but (big but here) NOT cutting it up. I'm re-using various connectors (EGR vsv, Idle-air-valve vsv etc) by building a small/short patch harness for each.
For example, for oil temp and pressure
I got an Idle-air valve male plug to plug into the harness female end. That will go to a pair of plugs for the oil temp and pressure sensors. No cutting of stock harness.
ECU <--> stock harness <--> IdleAir I1 female connector <mates to> IdleAir I1 male connector <--> OilPressure sensor connector
Yes I'm a geek. Whole google-sheets spreadsheet with all the connectivity, checks for pin re-use etc. If you're interested I can make a public version.