MS3 has no PNP harness, you'd have to wire it up yourself.
Other than that, the MS3 is far superior to the MS2. It has sequential injection (best the MS2 can do is batch fire), the ability to run coil on plug ignition, can support as many as 8 wideband O2 sensors for individual cylinder tuning, has an on-board SD card for data logging (you have to have your lap top plugged in to datalog with the MS2) and can be tuned using a USB cable as opposed to the MS2's antiquated serial cable. It also has (if you build it with the MS3X expansion board) 4 switchable inputs for launch control, table switching, data logging and NO2 control.
I'm in the process of purchasing the kits needed from DIYAutoTune to build one for my Ford 331ci Monster Miata. Right now I'm running a stock A9L which can not handle the extra 25 cubes. I see the process of building, installing and learning to tune the MS3 as an alternative to paying a shop to burn me a chip for the a9l. The total costs involved are not that far off from each other.
Check out DIYAutotune's site if you have not already. There's a lot of info there about the different systems.
Good luck,
-Jason