2000 Ford Focus Engines chugs between shifting of gears

So it does not chug when in gear? but just between them?

ORiginal clutch?

It chugs when I shift gears and also when my speed slows while in gear (say 5th or 4th while cruising the highway).

The Check Engine light has been on since I got this car but when it chugs it will flash until the engine sort of 'catches' and stops chugging.

I've only had this car since March so I have to believe this isn't the original clutch...

Okay...

This sounds like you are having a rich condition and need to address the cel.
When the cel flashes, most often too much fuel is not being burned getting into the catalytic converter. This will detroy the converter iof it already hasn't. The chugging is misfiring.

Need to get this diagnosed or start troubleshooting by getting the codes from the pcm.

Okay the "chugging" between gear shifting has ceased and the Check Engine Light is now flashing constantly. What is new is what sounds like a muffler problem and very bad gas mileage.

Could all these symptoms be a need for a new muffler?

When the check engin llight flashes, most often too much fuel is not being burned getting into the catalytic converter. This will detroy the converter iof it already hasn't.

Converter is prolly shot. Need to find what codes are listed in the pcm..I expect a po30x misfire code and Po420 cat code