Thanks, y;all! This has given me some hope that I can work through this thing.

I'm going to take a week off from cycling to get the ACL calmed down. In the meantime, I'm going to keep doing the weight work, but stick to closed chain stuff (no more quad extensions!).

When I do get back on the bike, I'll make sure to spin in those easy gears (no mashing!), and take my time to build up a base. I'm training for a sprint tri in September, so there's not really any need for me to do more than 20 miles or so in training right now. I think I need to wrap my mind around building my base for a solid year to get up to longer distances, instead of trying to do it this year...Plus a year of building the hammies can only help, right?

I'll also start looking around for some help with bike fit/sports PT. I'm not sure I'll be able to find this in my town, but it doesn't hurt to look! In the meantime, I'll order that book you recommended, Knotted.

At least I have a plan now!