The Warmoth neck will often need some levelling/final tweaking. They're not bolt on and go.
That said, if I'd seen this thread earlier, I'd have told you to get a Classic Player Jag HH. Locking button (or you swap the trem on *any* of the ones that don't if it's essential to you), decent buckers, coil blend.
The thing on the MIMs is that you buy the higher-end ones. Comparing the low-end stuff (especially the blacktops that cost less than the Standards) to the high-end is like comparing a Squier Bullet to the Mascis Jazzmaster. It's a huge, huge difference. On import stuff, you really do get more for the $$ once you leave the bottom of the price point.
For tuning stability as well, I'd have recommended the"Moved slightly forward" vibrato on the CP/Mascis/50th anniversary Jag/etc. It makes a heck of a difference - the CP I have is solid enough tuning-wise to function well as a guitar synth platform, which is far far more bitchy than normal guitar about that.
The Warmoth neck though will be fine though in terms of quality - they don't make junk. I haven't built a parts guitar in over 15 years, as I found what I wanted or had a tech do it for me (when I was working two jobs and time was > money for me, no way was I spending my limited time for music not playing instead). Big thing on any build is proper setup - be prepared to shim neck, etc, just like the factory would. And be slow and patient putting it together. Don't rush it.