Welcome Aboard Jamie. Assuming that the route in the body is flat on the bottom - I would use a hard block and sand down the 'top' side of the heel (as shown in your last picture) until it seats properly. Just do a little at a time until it is snug, but not tight, if that makes sense. I'd be willing to bet it only needs a small amount of material to be removed so it won't affect anything else.
With these guitars it is important to maintain the neck 'break angle' - this means the neck angles down from the front of the body a couple of degrees. So I would avoid fiddling with the bottom of the heel or the route in the body so as not to mess this up. Otherwise you may find there isn't enough downward adjustment on the bridge to get a nice action.
And yep, there are probably more glue spots than that one. If you wipe over the body with a damp cloth it can show them up more easily. You can use a product like 'goof off' and use a stiff tooth brush to scrub it off.
EDIT: Just casue it's easier to see in a pic than explain with text - this is what I mean by break angle - see on the two right hand guitars the neck angles back away from the body?
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