@jluna317 broken plugs ?
Did you check the plugs and pistons for contact? That males no sense at all.
The manifold is not very nice but there is no reason it would make so much of a difference for boost to the point where you are wearing out bearings and breaking plugs, to me that is totaly illogical. Something else is going on in that engine.
Is it your original engine that got forged or did you purchase the engine complete and already built?
Not trying to be a dick here, but seriously ,considering Alpha has not been building ecotecs for very long (compared to DDM or Hans) I would ask for measured specs and details of what they did down to torque used for every bolt when they built the engine, especially if they got a used block from totaled car and rebuilt it.
If they can't provide this that means that it has not been verified and to me this engine would be worthless, because there are so many things that could have been setup wrong you will be chasing gremlins forever and no one will be able to help you out without doing a complete teardown of the engine and make measurements.
Worn bearings, broken plugs, rods knocking and possible piston slap on a 5k miles engine makes absolutely no sense at all. This to me sounds like an engine that was just torn down, swapped rods and pistons, got bores honed a bit, adjusted ring gaps and put everything back together with nothing else done.
Where the cams removed during rebuild?
Where the hydrolic valve lifters drained before re-installing the cams? If not that could have bent a Cam on 1st startup (cuz lifters get hydrolocked and push on the cam).
So many little details that you need to check, just putting parts in and torquing bolts, thats not how you prep a performance oriented motor.
You might have worn tensioner or guides, streched cam chain, old oil pump, out of round bores, too tight rod / crank clearances, too much piston to bore clearance, pistons not having proper deck clearance, worn or improper crank to block clearance, bad crank thrust clearances, so many things to check when trying to figure this kind of issue out, you can't be just replacing parts without having measured everything and be sure you are in spec everywhere.
Again, my advise, as shitty as it is, would be to take out the longblock, tear it down and start from scratch measuring everything before putting it back to together. Its the only way you know for sure that it was done right, that you are in spec. In your case, that means builder takes responsibility for his build.
Do you have a oil pressure gauge? If not, get one and check oil pressure at the head. Worn bearings will usually make the oil pressure drop so its a good indicator.