When my plenum was blown, I had absolutely every problem you just described. Random misfires, flashing CEL, shaking in overdrive. It actually got to the point where I couldn't hardly use my overdrive because the engine shook so bad. I went through countless spark plugs, rerouted the plug wires, dumped more Seafoam into the tank than I care to admit and it was all just a temporary fix.
Here's the deal. If your plenum is leaking, you are going to have incessant running/driving problems. Fiddle with everything else all you want, if the plenum is leaking, NOTHING is going to help.
Here's another thing to consider. If your plenum has been leaking for some time, burning oil will have left significant carbon deposits on the pistons and combustion chambers. This crud is very insulating and gets very hot while running and these "hot spots" will cause detonation which, left to go for too long, can cause blown head gaskets, excessive bearing wear and destroyed pistons. Someone posted here recently about an engine that had running problems, tore it apart and discovered a piston with a huge chunk blown off which basically trashed the entire cylinder. Detonation was likely to blame. So, you have two options here. Pull the heads and clean everything or simply replace the heads, which isn't a bad idea anyway since your factory ones have a 95% probability of being cracked.
In my case, I had the heads replaced (yes, mine were cracked to hell), the pistons cleaned and had the plenum repair done. Ever since, no spark knock, no misfires, no weirdness. Since then, I've flashed the ECU with a tune that actually made the timing curve more aggressive, something which will exacerbate detonation issues (hence why Ryan will not provide a tune for an engine without the plenum repair). Still no problems.