sounds somewhat similar to the 20V MS mr2 i'm working on now...... i've reduced the problem to 1 of 3 possible things:

1) dirty/clogged (or not firing) injectors
2) timing belt position is off
3) coilpacks are bad

 

No settings have been changed in the MegaSquirt... and the car HAS done this before, but the problem went away after a few miles... so coil packs sound like a probable idea.

 

Ok, the plot thickens.
I pulled the cover and unpluged the plug wire closest to the passenger side... engine ran the same. I put it back, pulled the next one in... engine ran the same. I pulled either of the driver's side ones, the engine dies.
So, neither of the passenger side cylinders are doing anything.
I pulled the spark plugs, all have awesome spark.
So what does that leave me? Fuel?

 

Ok... I put the fuel injector plugs that were on the 2 good cylinders on the 2 that weren't firing, and the motor runs. So it isn't the injectors, it is either the computer or the wiring.

I tested to make sure I had 12v+ on all the injectors, I do.

Now I either assume faulty computer or wiring.

I hooked up the MegaSquirt simulator board, and INJ1 is blinking, INJ2 is solid. I think blinking means pulsing, which is good, and solid means there must be a problem.

So now I may be looking at a faulty MegaSquirt.

 

changing injector drivers in MS is relatively easy... i've had them go out on my last setup.... there are 2 drivers.... when you pull the MS unit out of the car there are 2 electronic pieces bolted to the side of the MS (that is, if you have a 2.2, green, board.... a 3.0, blue, board is different) using plastic screws.....

however..... your description of your test makes NO sense.....

megasquirt and edis both are setup similarly......

injectors 1 and 3 fire at the same time, injectors 2 and 4 fire at the same time... similarly... for dual coilpacks in a toyota.... cylinders 1 and 3 fire at the same time, and cylinders 2 and 4 fire at the same time..... it's a very simple wasted spark setup....

each injector bank (bank 1 is cyl 1 & 3, bank 2 is cyl 2 & 4) has it's own signal... but the signals within the pairs aren't broken up (ie... 1 wire comes out of MS and splits to injectors 1 and 3 to fire 1 and 3 at the same time.... same for 2 & 4, but that is a seperate wire).

the wiring on the coilpacks (from edis) is the exact same.... each coilpack has a constant 12V and each bank has a single fire signal....

so... if you pulled the plugs off of BOTH 3 and 4 and the engine did not change in characteristics... but 1 and 2 the engine died.... then there is something else doing on (ie, mechanical issues) or your description is inaccurate..... I say this because cylinder 3 is tied to cylinder 1, and cylinder 4 is tied to cylinder 2.... it would make more sense if 2 & 4 have the same symptoms and 1 & 3 have the same symptoms....


as for injector drivers (this is ONLY for a 2.2 board):

in the picture... what is labelled "A" are the drivers..... ignore the other letters (old pictures). Also, the 8-pin chip just to the right of the drivers is the chip that runs the drivers.... when that goes out they tend to cause the injectors to stay on.... not off.... IF this was happening in the car, the injectors would quickly fill the cylinders with fuel and probably cause the engine to hydrolock... i would know, i had that happen to me as well

good luck and let us know.... IMO opinion it almost sounds like a really bad HG leak between 3 & 4

 

You sure? Both 3 and 4 make no change when I pull the plugs wires or injector plugs... the engine is running off of 1 and 2 only.

 

i am sure about how megasquirt works....... i have wired up my past 87 supercharged personally.... helped wire up (but the MS itself is bad.... being sent out to have it looked at) a 20V mr2... have helped many other megasquirt owners as well and have looked over MANY people's setups.....

what i described above is how MS & EDIS work.... 1 & 3 are paired and 2 & 4 are paired (fuel through megasquirt and spark through the edis)...

scroll 1/2 way down for a wiring diagram:
http://www.megamanual.com/ms2/EDIS.htm
pin 10 is ignition signal for bank 1
pin 11 is constant 12V for coilpacks and edis
pin 12 is ignition signal for bank 2

http://www.bgsoflex.com/mspower/mspowercomplete.jpg
on the left hand side....
INJ2 & INJ2 are BOTH the same signal for bank 2 (injectors 2 & 4)
INJ1 & INJ1 are BOTH the same signal for bank 1 (injectors 1 & 3)

most people who use the relay board don't send a seperate signal to each cylinder from the relay board.... they will send one and split it around the fuel rail... this is how toyota did it from factory.... those are the signal wires.... the constant 12V is at the bottom (or right in the picture) and those are all just a 12V out....