Hi Tim,
its a bit hard to see exactly what the setup is in the photos but ST kits are designed to have a straight neck ie no rake angle unlike a G type guitar with TOM bridge has about a 3 degree angle. You may have needed a shim, or adjust the truss rod or adjust the bridge saddles.
The nut/slots look a little high in the photo.
I suggest you have a read Gavmiester posted a lengthy article on how to set the guitar up. The bridge saddles look too high so they are probably compensating the neck angle.
I've spent a fair bit of time helping Rozza set up his ST-1M he entered in GOTM. Its important the neck heel is well seated in the pocket so any drill shavings or burrs are removed.
Which way is the neck angled when looking from above when its lying flat, up or down ?
Also looks like the neck isn't straight and has up bow/relief (as Barge mentions) so probably needs truss rod adjustment