Chronic inside upper knee/thigh pain

[IceMan]

Hi Iceman, I have seen a physio who specialised in pelvis biomechanics and he said my right side of the pelvis was rotated forward a bit and that was putting a strain on my SI joint and giving me pain in the ligament on the rhs of the SI joint.
He gave me a muscle energy technique stretch to help this where you lie on your back and bring your knee up to your chest.
I think it was just my SI joint he talked about when he examined my lower back.

Yes but did he actually evaluate (and treat) your Lumbar spine? Problems in the SI joint and torsions of the sacrum are often accompanied by Lumbar problems (particularly L5/S1 issues if the sacrum is not moving as it should).

I stopped seeing him when I started getting knee pain because he said it was to be expected as I was re-strengthening my muscles, but I was struggling to walk and it was getting worse. And it turns out I was developing tendonitis above my knee cap and I should have been resting.

I would have stopped seeing him as well.

Another physio I saw a few years ago was unsure about my lower back and used to push into it with her fingers and say it was tight and a bit higher up it was too flexible when she pushed in. But she wasn't sure why this was but did wonder if it was linked to the nerve pain I was experiencing in my calf. She gave me neural stretches which helped my calf improve.

Just pushing into the lower back does not a lumbar eval make. A full evaluation might include range of motion testing in multiple planes, repetitive motion testing, segmental joint mobility testing, an assessment of alignment (along with sacral and pelvic alignment and dynamic tests), soft tissue assessment, muscle strength, reflex and sensation testing etc. The fact that neural tension stretches helped to reduce your calf pain is further suggestive of a possible nerve impingement in the lumbar spine. From all that you've said in previous posts it just doesn't sound like your lumbar spine has been adequately addressed.