I only just saw your follow up replies following my picture of the bridge pickup height.
I know I sound like a pain but it is very important I think at this stage to get everything right so I understand for my future builds
I'm going to adjust the bridge height much lower, retune, check measurements and then if all is good I will drill. I may need a shim in the neck pocket yet, but I'll check after adjusting the bridge.
I could barely hear the bridge pickup on my last LP build and it was around this height. This is the intonation guide I have been using that dingobass recommended: