I'll probably be buying a MS-I for my 99 using a CAS, completely replacing the stock ecu (we only have a snif test @idle, I guess the MS can handle that).
Only thing I'm worried about is idle. Will the MS idle correctly?
Also, is the code for a 99 in this configuration somewhat PnP? It seems the 'out of the box' code is for the 90-97 engines?

You will also need to deal with the alternator, the A/C, and the cruise control (if you have it) since those are also controlled by the stock ECU. But, it is no problem. Just go with the parallel AKA piggyback approach and let the stock ECU continue to control that stuff. That is what I am doing and it works fine.

Seems that the last couple of months, a lot has changed. I first intended to get a MS1, but now that the MS2 can use the stock sensors, I might go that route. I have no A/C or cruise, so I'd only need to sort out the alternator. I'm fitting the turbo by the end of the year, so who knows what happens by then :)

you don't have to worry about the cruise control, it runs on a completely separate system