Check plug for coolant contamination ie. is plug very clean, white maybe brown spots?
Check EVAP charcoal canister for liquid fuel
Remove vacuum hose from EGR drive miss gone?
Does your scanner have capability to monitor individual injector pulses?

when the light is flashing it is telling you that the potential for damage to the catylist is very high.in a situation like yours the very first things you need to do is 1= perform a compression test 2=perform a leakdown test to confirm/deny the integrity of the valve train.but i think i know what your problem is.you sound like a pretty handy person so what i want you to try is to either remove and plug off the vacum line to the egr valve,or remove the valve and block off the hole with a temporary cover(tin,aluminum,ect).then drive it like that and see if the problem is gone.i think it will be.what happens on these engines is that the egr passages clog up over time and these restrictions often force most( if not all) of the exhaust gases straight into cylinder four( just due to it's location)and this huge amount of egr gases causes a misfire due to the contamination of the fresh air/fuel charge.i am very confident that this will be your particulair problem.it's a fast and easy way to check it.and if that is not your problem then you need to have the tests performed that i mentioned in the begining of my reply,if this if the problem the you have to remove the upper intake and clean the ports.please let us know how it works out and thank you for choosing 2carpros.