Clogged cat, sticking throttle body or ignition?
 

143,200- miles currently on the car
140,000- Engine replaced
130,000- Coils, spark plugs, wires replaced and transferred to the new engine
Original cat

Upon engine replacement I was made aware of the throttle body that they had to clean to get it functioning and they said to be aware of it sticking in the future. They said they looked over the whole car when they did the swap, but I'm unsure if they dropped the cat and looked at it. Guess I'll call and ask about that Monday.

The car drove fine with full power for the first 3000 miles or so. I started getting a cel that would come and go, but didn't really notice any power loss. Soon after I noticed a stutter when accelerating over 6k rpm range and got a flashing cel. Doesn't a flashing cel signal a misfire? Pull in third gear is abysmal and overall power is down. Every chance I've had to take it to the dealer, the cel disappears, but at this point its not hard to recreate... Guess I'll take it to the dealer Monday, but any ideas?

Hello,
I'd guess your cat is bad. Flashing CEL is misfires.
Misfires kill cats.
Check out the misfire stickies here.

Get your codes checked first.
Free at most auto parts stores.

There is an 8 yr./80k miles warranty on the cat.
8 yrs. from date of original purchase.

Changing all 4 coils, plugs & wires would be a good place to start.
If your cat is bad, that's around $1400.
If you're out of warranty and not worried about passing an emissions test, you can replace it with a midpipe.

Hmm after reading my paperwork from the dealer I saw that they cleaned the ssv valve because it was stuck shut and said to keep an eye on it. After doing some research, that seems like the culprit...

Get codes checked still.