Yes, but I meant to call Best Western Rewards customer service (800-444-7646 according to my BW card, assuming you're based in the USA), not the hotel itself.

I don't know if you'll have any better luck there, but since it's Best Western Rewards that actually issues the points, it can't hurt to try. Even if they can't credit previous stays, perhaps they'll give you some points in compensation for not being able to do it? You won't know without asking them.

You're in a rare situation. In my experience (reading many hotel forums on FlyerTalk for way over a decade) most people either decide they want to join a hotel program on their first stay, or decide they don't want to join at all, or decide so much later that it's clearly impossible. That's presumably why no one else who has joined only after several weeks of stays has shown up in this thread.