Need a new fitness routine

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I used to train with a power lifter. I used to do yoga several times a week. I used to run for miles. I ran the NYC marathon last year. I used to work out for 1-2 hours a day, 6 days a week.

I got really sick this past spring with a mystery illness that impacted my breathing terribly. It caused me a lot of stress and I was very sick for months. Doc has now cleared me for all types of exercise, but the stress of working out in any capacity causes intense pain. My stomach hurts and I get head to toe muscle pain from any workout.

My list of "I can'ts" seems greater than my list of abilities right now as yoga and running cause nausea and lifting anything hurts all my muscles (not DOMS). I can only liken this to... if you've ever gotten into an accident: your muscles brace for impact and maybe you have no muscle damage after the accident, but they were so stiff from the anticipation of the accident that they hurt like crazy for no apparent reason other than lingering stress of the situation.

Any advice for starting over when my mind wants to be my old strong and capable self, but my body says no way?