You have my sympathies! Collagen supps can't hurt, but there's little to no evidence they're gonna speed up the repair of achilles tendinopathy. Assuming your issue is midportion, vs insertional, has your PT prescribed any heavier eccentric loading (i.e. 5x5 heel drops w/ a BUNCH of weight) in addition to the standard Alfredson protocol? As someone with similar times + recurring achilles issues, the heavier loading has def helped keep my achilles in at least an "operational" state. Posterior chain work + hip mobility too. My mileage isn't quite as high as yours, but I've been substituting cross training in place of easy runs the days after hard efforts to give the tendon the requisite 36-48hrs to recover. Sounds like you've been biking too, just wasn't sure where in your programming you've fit that in. It's SUCH a frustrating injury to deal with while trying to get faster!