What do you mean hardly would run? need details.
is the megasquirt board setup for seq fuel?

If the board hasn't been modified to run an aditional two injector drivers for fuel and is only using the standard two, under Advanced > sequintal injection change injector drivers to standard drivers.

Car wouldn't idle. Kept stalling and i had to keep the throttle up for it to keep running. The board is built for sequential injection.

Update: Cylinder one isn't firing for whatever reason. Tested the spark plug, ingnition wire and coil and they are all sparking correctly. Could be an injector? But car was running perfect before i parked it..

Could be issue with the MS and one of the injector drivers. I haven't dealt with seq fuel injection so you probably need to talk to brain and get some help on it from him. How you figure out cylinder one isn't working?

Pulled one of the ignition wires off and car was still running the exact same. All the rest kill the engine almost immediately.

Yeah I would talk to brain and see if you can help you figure out why its not firing. You could also use a multimeter to test and see if it has contiuntiy from injector to ecu.