By MS do you mean Megasquirt? If so it would be better NOT to abbreviate it in the original post as most people won't know what the heck you are talking about (about 90% of this forum runs carburetors). Assuming that is what you meant, I would use a stock harness and modify it as needed. After all, the MS will not be a plug and play operation, but will use the GM sensor array. You need enough wire to bring it to your Megasquirt and relay board. From there, it is up to you how you set it up. If you are not comfortable with building your own harness and all the custom stuff needed to run it, I would think twice about starting such a project. It can be done at home, but it requires sufficient technical knowledge and ability to be able to custom build it to suit your needs. There is no easy right and wrong way to do it, only many permutations of right and wrong. Al that being said, it is pointless to use a expensive aftermarket harness for Megasquirt. All you really need is the wiring for the sensors used (I think it would be: TPS, O2, MAP, CTS, and MAYBE BAR, but I think BAR is built in to the motherboard). That can easily be used off the donor TPI harness, and then all you have to do is solder about 30 connections to make it work right. If you can't solder, you have no business having anything to do with a Megasquirt setup. In that case, use a GM ECU and be done with it.
I would also post this on the boards at Megasquirt as you are far more likely to find someone with experience using a TPI with a MS ECU there than here. I know of it, and researched it for a bit when I was planning a ghetto turbo setup on a Nissan GA16DE in a B14 Sentra, but never went through with it.