yeah, the ms1 thing made me wonder, too.
i know that the ms2 daughterboard adds a $100 to the controller but i think it'd be well worth the additional expense.
i'm also well aware of the learning curve that goes along with developing a megasquirt project. it's one of those things where you don't know what you don't know when you start out. as you go along, you find more and more things that you want to add to your list and that requires changes to the original build.
i feel like i wore turbohull, sportage4x4, and other megasquirt guys out with questions over about 2 years as i was learning the actual workings of the ms2 and how it wanted to be set up.
there are an awful lot of other issues, too, like getting the communications stuff dialed in. that's what you're having problems with now. there are latency, delay issues with converting the old school serial communications to usb operation. computer operating systems like to assign ports and set up computer hardware allocations on their own and you have to know how to make the operating system live with the communications requirements of the megasquirt. it seems to boil down to the drivers associated with various usb converters. some work great and some just don't want to play well.
i even ran into problems with a controller mounted usb conversion board that was pimped as working fine with megasquirt. i had a very hidden problem with the usb board popping the controller into a virtual boot loader mode that would blow away the firmware and never let the megasquirt run without the laptop computer connected and running the tuner studio application.
what i have taken away from all of the time i've spent with the megasquirt project is that you have to achieve a certain level of expertise with the hardware and software. you go into it sort of blind, figure it out as you go along, and you learn which questions to ask as you go along.