Hi mate. I have built EX-5 & EX-1 as my 1st & 2nd builds.

The EX-5 had a few frets sitting high from around 14th to 18th and a couple of small dings in the rosewood fretboard but otherwise all good. I used all the stock bits to begin with and gradually upgraded everything except tuners as they seem ok. Wish I had discovered the recessed tele style jack sockets sooner as I prefer them to the oval plate that came with this kit.

When ordering the EX-1 there was an upgrade option to get the neck professionally setup and also got a bone nut upgrade too. Ticked options box for Grover locking tuners, Tonerider Alnico IV's, Bourns push/pull pots, gotoh 3 way switch, sprague orange drop, switchcraft jack socket, basically replaced everything except TOM bridge & stop tail piece. Also had same issue with neck placement but otherwise this was the best kit straight out of the box compared to 6 others I have built.

Sounds like your 7 stringer may have slipped through the QC net where neck appears to be the main issue.