Megasquirt is a DIY system. Depending on how much time you want to devote to getting it running its fairly simpleExpect to learn about how fuel management systems work so that you can troubleshoot problems. there is a ton of information out there on this system.
start at
www.megamanual.com.
here is a thread to my MS install. Does your engine look like this?
http://forums.pelicanparts.com/showthread.php?t=349639&highlight=efi+electric
I replaced webers with the EFI. It runs a lot better throughout the rpm range. Cold starts and off-idle response still need work but I have not spent much time tuning there.
The first thing I would do is read up on MS and then find a wiring diagram. Trace the electronics for the system. Find out what sensors you have. Find out how the injectors are wired. Find out how the vacuum system is plumbed. Find out about the oxygen sensor. YOu must have a wide-band sensor to make it work properly.
Next I would pull the ECU and buy the stimulator (~$75). This will allow you to sit in the comfort of your home and test to make sure all the functions work. At the same time you will familiarize yourself with the software and its functions.
YOu can then download the MS files and start programming the ECU. you will need a serial connection or a USB-Serial conversion dongle. An old laptop works great (W98). I can send you my files that will get your car running. Once its running you can start tuning on your own. Each engine has minor differences that you will adjust for. Mostly the tuning part is driving the car, datalogging the ECU, feeding the datalog through an analysis program and then reflashing the ECU. ONce you get the hang of it its pretty simple.