why not start with something like couch to 5k, where you intersperse walking with jogging at first?
also, dry needling is wild. my n=1 is that it is extremely effective at resolving referred pain. wish i'd thought of it last fall when i was getting those posture headaches (like i did the other day). something to seek out whenever the lockdown is over. no idea how it'd work for something as severe as what you have, or why the PT thinks it'd help fix your achilles, but i guess he's prescribing it for a reason.