blinking CEL and rough driving
 

My wife has decided to continue driving her 2000 Protege ES despite my warnings to leave it be.
Background: CEL has been on for a while, but it came up cat converter (sorry, don't remember the code) so we decided to forgo the repair at the time. This weekend it started flashing and running rough, i.e. shuddering and seemingly misfiring as well (?). I know it should not be driven at all, but there is no choice; seeing as the cat was getting bad anyway, I figure it can't be the worst thing.

So, is it probable that cat needs replacing due to being plugged, or is there perhaps another area that needs attention?
Thanks so much for replies!

This is now an 11 year old car and likely has the miles to go with that.
I understand that a blinking CEL means that the Cat is in imminent danger and continued driving will likely kill it. --But it has to get to that point first. So I am thinking this car has accumulated a long list of deferred maintenance.
I believe to figure this one out takes more than plugging in a scanner.
Is the cat plugged? --perform a pressure test.
Are the O2 sensors working --perform a test.
Is the throttle body all dirty?---visual inspection, clean with Throttle body cleaner aerosol.
EGR ports plugged? --open with wire.
Vacuum hoses leaking? -- replace them all. And inspect the old ones for clues.
Spark plugs, wires, coils: test, inspect, replace
MAF sensor: clean
Air filter: replace if dirty

You get the idea.

I would get a compression test and leak test to make sure that the basic engine parts are good before spending $$ on the peripheral parts.
Oh, yea: make her pay for everything! You can buy her flowers with the money you don't spent on parts and shop supplies.

Good luck!