What type of bike do you normally ride? Have you tried riding a different style bike to see if the pain goes away? For example, if you normally ride a road type bike with a more stretched out aero position have you tried a city cruiser with a more upright position to see if it alleviates the pain?

I am leaning heavily towards the too-long crank arm length.

I suspect where your issues are arising from is at the top of the stroke say 10 o'clock to 3 o'clock. With a too-long crankarm, the hip and knees are at really acute angles. Your knee can kick out of alignment and/or powering through the stroke can put a lot more stress on the knees.

Raising the seatpost can help alleviate the issue since it opens up the hip and thus the knee angle. Raising it too far however, can create too much extension for your leg, stretching and working your hamstring more and why your hamstring is now hurting.

Moving to a more upright position or shorter crank arms allows the hip angle, and thus knee angle, to open up more.

A bike fitting is probably a good idea but I would suggest finding a knowledgeable fitter who is comfortable with short cranks. I've found shorter cranks aren't even on many "fitters" radar since crankarm length is limited by the OEMs (Origin8 has a good selection of ahort arm triple and double cranksets) and they rely too much on "general" fitting procedures and/or software.

You could try a cheap used city cruiser off CL or borrow something similar to see if that helps as well.