It starts hard (does a lot of cranking before, or rotates and sort of stops when cranking?)
Injectors were cleaned on the bench, no testing
Only 2 and 7 cylinder look good, rest are black

With connectors on with correct color and it runs worst, have you tried to set timing, and if so did it also die?

With this true, then either its out of time or wrong firing order, or someone has messed with the harness.

https://cimg4.ibsrv.net/gimg/www.off...e74fd33a7d.jpg
Each injector bank should fire every 90 degrees of the crankshaft rotation in alternating occurrences.
It runs bad and has no power

This all said, with water getting int the oil, this needs to be found before anything else, and would expect the intake first

Im presuming that the mefi 1 is put into base timing mode like the 3 ?? when setting timing, if doing this and it wont run at 8* there's a timing, firing order issue, I dont know how CP can modify the ecm timing and fuel tables, spec the cam and it run perfect, is the valve lash to tight ?

SPC INSTR 1 ?
SPC INSTRC 2 ?
SPC INSTRC 3 ?
Camshaft doesn't have swapped firing order does it?

I would have done things a little differently. I would have rebuilt the motor and got it running with an unmodified ECM. THEN tune it to the motor. Right now there are way too many variables that have been changed. It would not hurt to have all the injectors cleaned and flow tested to verify their flow rating too. Make sure the distributor is in correct and that the base timing set in the MEFI 1 matches what is physically set. You may have to rev the motor up to 1000-1200 rpm to get base timing set. Having said that with water involved there are likely bigger issues. Intake gasket secured?

The computer had been modified before it came in the door, so I was just trying to find something to match the program that was in it. As far as the intake goes, I was pretty anal when I put it together. I talked with a Mercruiser guy that told me the fuel injectors have to be timed as well as the ignition timing, but I don't know how to do that. I never thought about throttling the engine up while it's in base timing mode. I will try that.

Alldodge, it was my understanding that the injectors were batch fired, all the green/reds at the same time and all the blue/reds at the same time.

Liberator221, What does that mean?

I think it goes into base timing mode the same as the 3, but have ever worked on a 3, so can't tell you for sure. As far as the valve lash, anything is possible. I just did it according to the Mercruiser service manual.

Agree, but the batch is every other cylinder, Red is constant power, and the blue/green applies a ground to fire injector
Cylinder
1 - batch green
8 - batch blue
4- green
3 - blue
6 - green
5- blue
7 - green
2 - blue

If it fired with your wiring
1 - green
8 - green
4 - green
3 - blue
6 - blue
5 - green
7 - blue
2 - blue

I agree with AD, get your timing set correctly and place the injector caps as the factory spec's it outhttps://cimg2.ibsrv.net/gimg/www.off...dc6324e880.jpg