Oh you deffinately still get junkyard components, but with the MS you can get throttle body from this car injectors from that car ...
Right now I'm running 22lb new takeoff injectors from http://www.fiveomotorsport.com, an isuzu (gm) throttle body (only one I found with ported vaccum ports, still running stock EI distributor), lc-1 wideband o2 from innovate motorsports - you get the idea. The megasquirt uses gm sensors by default but you can calibrate it to use any you want if you have your heart set on something else
CStryker - progress on the megasquirt is made too quickly to say "I'm going to wait for....." by the time gpio board comes out a new gismo for it will be in the works you want to wait for, and the cycle continues. IIRC you can get everything going with an MSII/V3 board now, and add gpio later.
Also check out www.diyautotune.com and www.rs-autosport.com for actual ms hardware, and www.apeusa.com for fuel delivery.