No bueno

Hi, I've had my VC 3.1 300 for a couple of years now and it's had some pretty crap meshes since I've built it at about 0.35mm variation. I've built the printer with badly printed parts so I just thought it was the cause and since it printed very well I just left it that way. I've recently come back after a one year break from printing and I've decided to rebuild the printer with solid PETG-CF parts. I've just rebuilt the entire Z axis and now it's even worse at about 0.5mm variation. What do you guys think is the issue here? I'm suspecting a twisted gantry, could that be the answer? I'm adding two pictures, the first one is a mesh before the rebuild and the second one is after the rebuild. I'll be very thankful for any help.