Could still be the hams. Could also be the peroneals (lateral calf muscle). Any lateral foot pain (5th metatarsal area)?

Look at how much of a heel drop style you have, knee tracking, and fore/aft position as well as height. Too far back strains the backs of the legs, too far forward usually cases quads or medial/anterior knee pain.

You can strain the peroneals if you pronate (or supinate if there's too much stretching), and that can be a lateral cleat position thing (foot too close to cranks, for example). You can also strain them if your cleat is too far forward (pedal axle should be a few millimeters behind your first metatarsal joint). Look to see if you have any forefoot abnormalities or anything else that would affect your knee alignment. If that's ok, then look at your saddle adjustment.

I find it hard to believe that you've blown out both LCLs. Despite all my blabbing, I'm no expert (just frequently injured), but something muscular on both sides goes more with the odds.