first thing I notice - it appears that your router bit is WAY too far out of the collet for a bit that long

unless you have an extra inch of shaft hidden in that collet, get that bit down into the collet where it belongs
next - you're missing the base plate. you can make one from a laminate topped piece of mdf, or make one from acrylic/plexi ... either way, that should be in place if nothing else to allow your router to slide on the template while giving you a solid base to keep it from teetering
then, here's my preferred workflow ...
- use a Forstner bit to remove the bulk, staying 3/16" - 1/4" shallow so you can clean the bottom with the router bit (and not leave any dimples from the Forstner bit. I also leave about 1/8" on the sides, and don't worry about it having a series of scallops. forget the chisel - that's why you're using a router
- use a 1/2"D bit (I prefer a mortising bit) with collar bearing to follow the template edges, but keep it about 1/32" off the roughed bottom for the first pass. the intent here is to define the edges so they are clean
- adjust the bit so that you dig into the bottom to a depth that is 1/32" shy of your final depth and remove all the wood giving special attention to the edges
- adjust the bit to final depth and remove all the wood giving special attention to the bottom so that it's smooth
- I then follow-up with the StewMac 3/8"D corner bit to radius the corners to fit a typical Bart/EMG shell corner radius. I clean the corner in two or more passes depending on the depth of the cavity
when routing a super deep cavity (like for a Nordy Fat Stack) you may find that you need to remove the template to get your final depth without hitting the template with the router collet. in this case, simply clean the edges like it was the 5/8" deep cavity above (don't forget to do the tighter corners), and then remove the template and used the edge of your cavity as the guide to finish routing to the final depth.
DO NOT simply extend the router bit out to accommodate the added 3/8" of depth - this is a dangerous thing to do, as a bit that long needs to be held securely in the collet and not just pinched at the end
all the best,
R