never used MS but i have heard its pretty involved as far as setting it up goes. have to make your own motherboard i think and make your own wiring harness etc. that sort of stuff if what i have been told. but it does work well once it all going.
i have used a tweecer, and its very capable. the tweecer RT is 550 new. but to really take full advantage of tuning, i'd suggest a WBo2 ( a must if you plan on getting serious with tuning) and some better programs to use with the tweecer which can be bought for around 120$, which are worth it. so in reality you can have around 750-1000$ wrapped up in it all depending if you buy the tweecer new and what WB you get. but to me its worth it. the tweecer works very well and gives you control over everything.
i could go into great detail but i wont, if you decide to get a tweecer, theres alot of support for it online, plus i can help you also. if you need any help shoot me a PM, i'm no tuning expert but i know my way around the tweecer pretty good and did the whole "start from scratch" thing, so i should be able to get you on your feet.
as far as your mods. N/A they may work alright, but going forced induction... its pretty much required to get a tune if you want your setup to last long. i ran my supercharger setup last year untuned, i thought it ran awesome, didnt have a tune for it, i ended up popping a head gasket. i finally got the tweecer setup and the car ran harder, drove better and was safer (as far as engine damage goes)