Before I take the guitar into a pro, I'm going wait for my tools to arrive and remeasure everything. One thing that folks have mentioned is neck angle, which got me thinking. The Gotoh 510 bridge requires an angled neck pocket. In fact, per Warmoth the Gotoh requires an angle of 1.5-3* to be cut.
However, there is one aspect that confuses me a bit. First, the site says selecting the Gotoh bridge requires the angled pocket and implies it's accounted for in the build, however, the site also says this is a $10 add on. I'm not sure if the neck pocket is automatically routed if the Gotoh is selected, or if it's an add on which the buyer must select. I'm also not sure which direction the pocket is supposed to be angled, but it sounds like if it's flat or cut greater than 3* an ideal setup can't be achieved without further modification.
More measurements to confirm, but maybe this is part of my issue. I bought the guitar second hand, but it was a custom build. The body and neck were ordered together, the Gotoh was clearly called for, so I hope all the variables were accounted for. Being a rookie setting the guitar up, I'm almost certain I've messed something up along the way, but you never know as there are only so many levers one can pull.