My work schedule makes it nigh impossible to get hands on car time. :/
Quick question..

The backfiring, rough running, flashing light...
This is definitely more than a vaccuum leak right?

The last time I saw all those same problems there was 2 wires hooked up to the wrong plug. It ran but rough, and back fired threw the exhaust.

Yep, easy to do. Double check all the wires and make sure they are on the correct plugs. Also, the flashing CEL indicates an active misfire. If you pull the codes it will probably lead you to which one(*) are the issue.

Jay

Plug wires are all connected to right areas.
Saturday I'll have a full car day...this is just an overview before work. But, the engine gets hesitation(at least half a second or a second after I step on gas before it reacts) and the choppy running rough sound after I switch it into gear. If I just turn it on and leave it in park, it runs a little rough but not like that.
Anything I should look at Saturday?

Also..
Broke tab off the IAC sensor. The connectors still connect in firmly, but do I need to buy a new connector with a tab? Or is it okay to have a tabless one?

You run the risk of it coming unplugged.and it loosing up and allowing moisture in

Nah, the broken tab shouldn't matter as long as the connection is tight but I would look into replacing the connector at some point.

Other than checking for vac. leaks on Sat., I would give all the connections a once over, check the PCV, and then find out which cylinders were misfiring. Might come down to a bad coil pack or ICM.

I checked PCV last week, it rattles=still good right?

Here'* a final overview(and camera is charging so I should get video soon):
1)Car had MAF low voltage code.
2)Car then developed flashing SES light, heavy shaking in gear, running very rough.
3)One coil pack was rusty.

Ruled out:
1)Cleaned MAF sensor/checked voltage, everything'* good there.
2)Replaced coil pack/#3 plug.
3)Replaced MAP after breaking it to check PCV-checked PCV-rattles.

Things I'll be checking saturday:
1)Changing oil--oil is low, due for change anyway, and need to check for metal/coolant.
2)Vacuum leak--none visible up top--leaves EGR, manifold?, what else?
3)check other plugs.
4)get codes read.

Yep, rattle is good. Does it have both o-rings in place still?

If you haven't done so already, with the car running in Park, spray carb cleaner around all vacuum fittings, the edge of the LIM/UIM, around the TB and any other places that vacuum could leak and see if you get any spots that make the car run differently. If so, then that'* a leak.

From your list it sounds like you have the rest under control. Hopefully one of these tests will show the issue. Good Luck

If I asked this already, sorry. Have you unplugged the MAF and start the car? It will run rough stumble and then settle down. If it runs better unplugged then the MAF is the problem. had a car here a few weeks ago, ran rough, had a miss, but coils tested good. Swapped out the ICM and the car ran great.

As for the plug, best to change it out. But if you put dielectric grease that will protect it from corrosion.