You can do a megasquirt for a fair price but the cost adds up quick. Depending on which MS unit you want, you can spend 120-250 on one of the standard controllers, another 200 on a wideband o2(a necessity IMO), then you've got to scrounge up an intake w/ injector bungs or have one converted, fuel injectors, fuel rail, high-psi fuel pump, regulator, probably want to sump your fuel tank, throttle body(pricey unless you can figure something out cheaper), the list goes on. You hit the 1k mark before you even get started. Then it's a diy project so you have to sodder together your efi controller, wire it in, rig up the fuel system, etc, a lot of effort. If you were very thrifty you can put one together for $1000-1500 depending on what you can get and what you can do yourself.

EFI is good and efficient on stock and mild motors, but once cam specs start getting really wild, it has a harder and harder time adapting. Especially a speed density system like megasquirt, which uses manifold vacuum to calculate fuel delivery. For motors with too low/erratic vacuum to work well with this, it has a mode to use throttle position and rpm to calculate fueling. So if you have a cam that's large enough to make tuning a carb difficult, you can't expect it to be as easy as pie to tune in efi either.

If that's what you want, go for it. Just remember it'll never be as cost friendly as your carb and you will have to spend time tweaking with a laptop to get it right.