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Ohm20 has done a deep dive and I am sure can attest some (most if not all) of the indications require some complex, thoughtful and time consuming work to arrive at a well engineered trial protocol.

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You want to set up the trial for the best chance of success. You tailor it based on the known MOA and if it's phase 3 based on phase 2 results. Endpoints will be based on what your drug has the ability to resolve. Inclusion/Exclusion criteria are critical, if there's a group that won't enhance the endpoints exclude them. The failure in CD10 was certainly based on not excluding those showing zero or few symptoms. But if you have everything to narrowed the FDA might not accept the protocol so balance is needed.

Let's take longhaulers as an example. The FDA has guidelines for ME/CFS trials that are the nearest thing to longhaulers. The main endpoints will have to be based on solid scientific tests not on how much better the patient feels. There are tests in use for fatigue, cognition and the other myriad of symptoms. Using those you set a baseline for what would be considered meaningful improvement. If biomarkers can be agreed on with the FDA then use those as secondary endpoints.

With inclusion/exclusion criteria Dr. Recknor has the complete results from phase 2 so he should be able to narrow things down a bit.

Now you have to convince the FDA that your trial protocol is solid and scientifically valid and hope they aren't sandbagging you.