Last year I didn't have any major knee pain issues when I got my trike.

This year when I started out, my knee was hurting above my knee cap. It felt like a muscle related issue and I assumed it was conditioning related.

Then I got clipless shoes, and the knee pain has moved to below the knee cap, on the front of the leg.

Not sure where to start with adjustments. The cleats are currently all the way back, but I'm not sure if it's cleat position or maybe I need to adjust my boom length due to the new shoes. My leg extension feels pretty good, but maybe I need to move a small direction in one way or the other.

Thoughts?

IMO your first adjustment is to throw those damn clipless pedals ,and shoes, in the trash! Then install a pair of BMX pedals like these...........

https://www.nashbar.com/bikes/Product...=c&cagpspn=pla

Once the BMX pedals are installed your knees will stop hurting.

I was using BMX pedals and I still had knee pain, just in a different spot.

Plus, I like the positive food retention on my trike vs the heel slings I was using.. if I hit a bump and I was trying to pedal, my feet should shift and I'd have to stop pedaling, lean forward, and re-adjust my feet and the heel sling.

Nothing wrong with clipless pedals. But it does sound like you have a serious fit issue somewhere.

For me, pain below, and inside, the knee means either the saddle height has slipped down or my (Speedplay) cleat(s) have moved away from the bike. For a KEO or SPD-SL cleat improper positioning could be the culprit I suppose.

I think OP is riding a recumbent bike. Very minor adjustments of boom length can solve this. Probably longer.

I was looking at this earlier this morning. Using the rough guide from the bike shop I bought this from, it should be pretty close to the right length boom, but obviously something isn't quite right. I'm getting similar leg extension to what I get on my upright, which I've never had any issues on.

I'll see if I can move the boom out 1/4" or 1/2" and see what happens. I might need to lengthen the chain though.

On an upright bike pain above the knee "usually" means the seat is too high, and pain below the knee that the seat is too low.

On an upright bike, as you press down on the pedals weight is lifted upward, and the hardest you can press is limited by your weight (and to a degree by pulling up on the handlebar.) On a recumbent bike your legs are pressing against the pedals and cannot push your back any further than the seat back. In other words there is no natural safety release for pressing too hard. If you have really strong legs you are unlikely to hurt yourself on an upright bike, but you can easily damage your knees on a recumbent if the muscles are stronger than the tendons and ligaments. Additionally, you are using different muscles in different ways on a recumbent. There are several ways to hurt yourself on a recumbent if you just jump on and expect to ride it like an upright bike.

My wife and I have proved this to our satisfaction over a period of many years. She rides a TRICE now and we just sold a Rans Rocket and a Lightning R-84. As I type this my patellar tendon is crying for attention. Our last Labrador Retriever had to have an anterior (caudal) cruciate ligament tear corrected surgically. She never rode, but she spent a lot of time in a recumbent position.

So my old shoes I had too much boom extension, and my new ones I need more? I'm having a hard time wrapping my head around this since they don't feel much different.

I do have 2 rides planned in the next 2 days, so the platforms are going on for Wednesday's ride, then back to clipless for Thursday. It will give me a good comparison with the greatest likelihood of completing both rides without major pain.

right.For a KEO or SPD-SL cleat improper positioning could be the culprit I suppose.

Well, darn! At least you tried BMX pedals already. Could it be that you need to go to the doctor to see what's going on with your knees??

My knees are fine when I'm not cycling.. so I know cycling is causing it. I just need to figure out why. My doctor will order a bunch of tests by the time I know anything, my season will be over.