[krisj144]

I'm not too familiar with your hydra ecu, but i know on my AEM unit I'd only have to re-set the base timing when I use adjustable cam gears that are adjusted from factory specs on the evo since the CAS is non-adjustable unlike the 1g dsm's.

Are you using adjustable cam gears?
Which cams are you using?
Have you checked the literature that comes with the ecu to see if you need to re-set the timing in that unit?

I highly doubt that your cams were keyed improperly, it's more likely installer error, though you did say that you double checked all the timing marks after the cam install, correct? This is to say that you've made certain that the crank and oil sprockets match the cam marks with the dowels at 12 o clock right?

 

[krisj144]

if the cam sensor was reinstalled improperly after the cams, it would either be 180 degrees off or in phase. no other possible way to do it.

My guess is that if it is installer error and not the ecu, which I'm not claiming is definately the case... then the cams are off a tooth. With the dowel pins on the cams at 12 o'clock, the marks on the cam gears should line up directly with the valve cover. This is easily checked by simply removing the upper timing belt cover and turning the engine either by the access hole through the fender liner or bumping the starter.

I think you need to check the mehanical side first, then read any literature that comes with the ecu as far as needing to set base timing and so forth.