You could just try a power balence test on each injector to see if the shake doesn't get worse when you loosen each of them. If nothing else it would narrow down the problem to that exact cylinder (if it is indeed a problem that is isolated to one hole).
When I first started my engine after dropping it back in, there was some blowby (comparable to when I tore it down), but it settled into a smooth idle in seconds and waited patiently for me to take it out for a spin.
I did take the truck on some hills and did the usual hard acceleration with engine braking to slow back down. Did that for a few days in a row and kept a close eye on the pyro since you don't want the EGTs to get too high early in the break-in. I've been told it can cause a premature glazing to build up in the cylinders and prevent rings from seating. And whatever you do, don't run straight veggie oil on a break in either.