Complex issue

Okay, so where to start? Well, early 20's I become interested in going to the gym, after a sedentary lifestyle, lots of computer games etc. I joined a gym and started to lift weights, with particular emphasis on the compound movements. My programme I was given was essentially a 5x5 routine across mon/wed/fri. This would include

Low bar back squat
Bench press
Pendlay Row
Deadlift
Overhead Press.

Now, i began getting various aches and pains, sharp electric shock sensations, sore knees, pulled lower back various times etc. i began to research what was going on, because in my head I knew how to implement safe positions but my BODY wasn't allowing it. So for example rounded lower back when picking up the bar for the deadlift, rounding during the squat etc.

I saw a physio who told me okay, you need to go away and strengthen all of the muscles at the back of your body and stretch everything at the front. (I now know from my new physio that was twaddle that was "popular" advice at the time)

So... here I am at 30. Persistant lower back aches as I walk, stand and do anything a functional human should be able to do. Neck aches, and just can't get in a comfortable sleeping position.

I have JUST found a FABULOUS Physio and I can't stress I finally feel like he gets me he understands the issue. I think partly because he's familiar with the exercises I was trying to perform. So.… his diagnosis is this.

Basically, nearly all the muscles in my body are all out of sync and imbalanced. He explained that the body is VERY clever and WILL find ways to adapt movements. I'm looking at a 2 year rehab programme at least.

He said my upper back muscles aren't "doing anything"
My glutes are substantially weak
Hamstrings are weak
Quads are weak

He said did various leg tests and he said "You've HAD strength and power there and while yes you are resisting my force, that's muscle memory not actual power"

Step 1. Long term insoles which I now have.
Step 2: Strengthening programme.

So, I am now stuck on a leg curl, press and extension machine.

On the leg extension at 20kg, my quadricep muscles are like I have Parkinson's on the downward phase of the movement. The full machine was juddering.

Hamstring curl i'm doing about 15-20kg at a push but they will cramp...

So all in all, I just wanted to ask... does this sound like I'm on the right track with the advice given and if anyone can explain how my issue has occurred and if what he is saying with a combination of insoles and machine weights, i'll be fixed.

Step 3 is hack squat and glute hamraise
Step 4 is Trap Bar deadlifts
Final step: Back to traditional compound movments, injury free.

I'd love a big response to this as this has been going on for years. I was told by the chap that he said to be fair to traditional Physios "You're pretty complex mate"