Been reloading lead for over 30 years and never had a BLL this high. Will be 64 this year so I may start loading jacketed bullets. I don't like loading with gloves on, may also try that.
If you changed from lg primers to small primers did you also change the primer tube to the correct one. I forgot to change the tube once and had the same problem. I was checking everything I could think of the last was did I change the tube? nope I forgot.
I don't understand why a custom built gun would need a 1000 rds through it before you can expect the proformance it was built for.
another few minutes polishing the parts should save the need for breaking in.