My 2c on the matter.
Firstly, the reason you can’t do the base timing is because there are error codes in the ECU. I had a similar problem after doing my manual conversion. It was impossible to set timing as the mark just kept on jumping around, and seemed to be in a different spot every time I checked it.
This was all because I have a wiring error when I bypassed the neutral starter on the ECU when I did the conversion.
If I did a self test on the ECU, it would spit out the neutral starter error code, and exit. The ECU is most likely looking for some sort signal input form the AUTO.
So what you will need to do first is get a 3.9 MPI ECU in there and get rid of all error codes, then set your base timing. Or, you could try to get rid of the error codes with the existing ECU, which ever suits you.
Now, when going from an EA Head to an EF/L head, it's pretty important that you have the head decked, and use a thinner head gasket. This will give you back your compression. Remember that the EA sits at 8.8:1, and anything lower then that aint going to help you out in the kW department I assure you.
It would also be a good idea if you installed a variable cam gear when using the EF/L cam, or any non standard cam for that matter.
The reason you have lost power down low is because of the cam profile of the EF. The EF's ECU has the ability to alter timing at different rpm. It has a similar profile to the ED XR cam, which helps at the high rpm end, however it relies on timing alterations down low, and the dual runner manifold to give it some grunt.
On the other hand, the 3.9 cam was developed to work with a 3 speed, and 2.77 gears, with max power at 4500, and no timing alterations, which is probably why its gong better down low with this cam.
With a variable gear, you should be able to adjust the cams power range so that it gives a bit more life down low.
Keep Us posted.
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