The frustrating thing is that for the last week and a half I have been able to walk up and down stairs at work, check the mail, etc and felt fine. So I expected a little better than 2.5 minutes of soft pedaling on the trainer.

What are you using as an SpO2 sensor?? Do you have a decent finger tip based one??
As an anaesthesiologist this is bread and butter for me, you can get interference from a lot of things. Just want to make sure that number is real.
If it is real, then I would definitely be taking it super easy and not doing much else just yet.

I bought a Wellue O2 Ring. I wear it on my right middle finger.
It's kinda in line with my garmin overnight readings from my wrist. That had me down to 88% at some point last night. I really think the sickness is impacting me on top of the clot.

I have just checked them out, they seem OK.
Just be cautious on both fronts. The sensors are subject to a lot of motion artefact, so it can be difficult for them to provide a reliable reading during exercise, even if you think you are holding nice and still. I would suggest, if you get a low reading during exercise, just to pause and look at how quickly it returns to normal.
In terms of what is happening overnight, have you ever been diagnosed with obstructive sleep apnoea? It is a bit of a worry if you are dropping down to 88% overnight. You can look at some risk factors for OSA by a quick google search for STOP BANG, that will give you online scoring systems which will tell you what your risk is.

Do you have to wear the SpO2 sensor? Doctors orders?

I just feel like I would be glued to that in an unhealthy way, even knowing that it's not 100% accurate all the time. I wear a Coros full time and the first several months I was paying attention to heart rate way more than I should have. My resting heart rate is super low and occasionally it shows me a heart rate I know isn't true. It's not as accurate when it's not in workout mode. Not worth stressing over it.

If you're allowed to train don't worry about Z2 stuff or trying to gain fitness back. Start with short & easy sessions. Try every other or every third day. Listen to your body. You can come back from this. You don't have to do it all at once.

Yep. He said to make wear it and make sure it stays above 90% and stop activity if it goes below. I was HOPING to be able to hit Z2, but at this point I just want to be able to do something for a few minutes without that alarm going off.

Have never been diagnosed with sleep apnea. Before this all happened, I was consistently above 98%, even when I had a big bout of COVID. I really think it's a combination of the clots and this cold, which is causing some minor congestion. I picked up an NSAID free decongestant yesterday. Hopefully helps.

Totally Agree with this. I had a number of trainer rides that ended up on the bathroom tile trying to cool off feeling completely sick shortly after getting out the hospital. The recovery can take a lot of time with this, so patience is crucial. I tried to rush things and it wasn't pretty. The thing that stuck out to me was that some people see a PE as no big deal, some as life threatening. When I had it it seemed like I was an anomaly and no one knew what to do with someone who was in shape and under 60 (I was 42). It was after I was pretty much back to normal that I started seeing it pop up in articles with endurance athletes. The recovery can be seen as equivalent to a significant heart attack for some people, so I'd recommend just being really patient and mentally wrapping your head around a year. Might be less, might be more, but letting go of trying to be what I was right away helped a lot mentally.

6 months post clot, the weekend before Thanksgiving I ran a 5k and finished in 23:30 on a long course. A bit slower than pre clot, but I was happy to be able to do it. The last mile hurt as it always does, but I had flashbacks to the first few days sleeping face down on the couch propped up with pillows. Legs didn't have the juice, but there wasn't any quitting.

So on this Thanksgiving weekend I am thankful for this thread and the people is led me to meet and for the journey back.

Awesome -- glad to see you back! Keep up the good work!