There are a number of options out there. I am only familiar with a few and only on a pretty surface level. I know the most about MS but still don't know a lot. I have been about halfway through a MS3 build for about a year and a half now. I need to get the daughterboard before I can finish it.
The MS3 is awesome and has more capability than most will need, The main reason I went with it is the ease of doing sequential injection and the fact that it can be setup for internal knock monitoring and the knock module is supposed to be pretty good. I haven't read much about real world testing on the knock module though.
MS2 is enough to get a motor running quite well and do everything most people would need to do.
The DIYPNP requires assembly but plugs into a stock harness. The advantage is that during tuning or as a failsafe you can always plug your ECU back in and get around on that.
The MS PNP is a little more expensive but comes assembled.
I have been hearing a lot of good things about the AEM EMS4 lately. It should be able to do everything almost any 4 cyl owner would need and is a pretty great price.
I can also get a Tweaked plug and play harness made for it if you wanted or if you want a cleaner install you could get a whole engine harness made for your motor/chassis.
http://matrixgarage.com/?q=store/engine ... ning-toolsThere is a great MS comparison here.
http://www.msextra.com/feature-xref.htmlAnd a lot of info on the EMS4 here.
http://www.aemelectronics.com/engine-ma ... system-58/