I had some similar problems with my experiences with Seymour Duncan's and Dimarzios, I'll share my experiences and solutions with them.
In some guitars I have installed Dimarzios in (i.e. s7420, rg7421, etc.), the wires would come through the baseplate and stick out the corner, so that the pickup would not sit flat because the wire was sticking out on the bottom. So what I did was pull the wire and sleeve back through the baseplate so that it doesnt go through the baseplate and protrude on the bottom anymore, it actually sits on top of the baseplate and runs right next to the coil. On guitars that had dimarzio new 7's installed (i.e. rg7621, rg7620, rg1077xl, etc.) I didnt have this problem because they already had dimarzio's in them so they were already routed to accomodate for the cable coming out the bottom of the baseplate.
As far as Seymour Duncans go, the pickup mounting tabs are much taller than any ibanez stock pickup. The pole pieces extend past the mounting tabs of the pickup, so you have to route 7 "holes/pools" underneath the pickup in the pickup mounting cavity to accomodate the pole pieces. Even then, when you mount the pickup and screw the pickup all the way down so the mounting tabs are pressing against the body wood in the cavity, it will fit but it will be VERY close to the strings. The only way to make it go lower is to either route deeper the rectangular portions where the mounting tabs are so they can go deeper, or bend and cut the mounting tabs so that they are flat instead of in the L-shape, so they can mount flat.
I suspect that this is the problem you're having with the Bareknuckles. They should mount fine, as long as you route for the 7 pole pieces if they extend past the bottom of the baseplate and mounting tabs, but like I said the pickup will most likely sit very close to the strings. The only cure for this again is to either route the route for the tabs deeper, or modify the baseplate/mounting tabs. To get an idea look at a Jackson DR7/DX7. Those have direct mounted duncan designed pickups with the same type of baseplate with the extended mounting tabs. The routes where the tabs go are actually deeper than the route where the pickup actually sits, so that it can go lower.
Hopefully this helps some.
EDIT: Crap, you already got them put in! Taking forever to write out a post FTL!
