Well, if I wanted an Eric Johnson Strat with a short scale (I don't, really) I'd do the same thing. There are a lot of professionals playing Johnson, Beck and especially Clapton signature models, the latter because of the active mid boost that really does get you through a set of bar band songs originally played on Gibsons. One reason for going to a signature model is that the quality control just IS better - the pickup's outputs are already matched, the electronics are too. I would guess that the Johnson signature is also very carefully-designed so that the neck fits just perfect - which means an aftermarket neck may not. (These little things are pretty common, by the way - a few years back someone else had this exact situation.)
In this situation, I've seen people use a shim that raises the entire neck up. A quick way to check this is to use an extra neck plate inside the pocket. If that works, you could think about making a tapered shim. However, that takes some level of precision, it's an extra piece, the neck is connected with a slightly-shorter number of screws.... yuck.
If it was mine, I'd buy another pickguard for $15 and cut out the part under the fingerboard. And then if that works (which assumes you have figured out the problem correctly + there's now extra room left) I'd personally also reshape the neck's butt end so as to not need the shim anymore. That also required a fair amount of precision, and two straightedges you trust.... if the contact is really minimal you could also just take a bit of wood off the bottom of the Warmoth's fingerboard overhang. I would FIRST make really sure that that would fix things and you'd have to be careful not to sand the butt end - it looks like you could get up to 3/32" more clearance that way.
What I would try to avoid is changing any of the original guitar's parts, because it is worth a lot more "stock." The Eric Johnson neck only has 21 frets, right?
(By the way, on Eric Johnson's 2006 video he plays "Cliffs of Dover" on a old GIBSON SG/Les Paul - and it sounds just like Eric Johnson, playing "Cliffs of Dover." Which is elliptically why I don't want an Eric Johnson Strat - it wouldn't help. :sad1
