More bacon and cheese! Also, use the sharpest Cheddar you can.
I think that many recipe-writers keep the “bad bits” to reasonable amounts so people won’t immediately dismiss the recipe as too fattening. Sometimes you’ve just gotta go for it. The bits of fried cheese (the parts that make contact with the waffle iron) should have a ton of flavor, just use more of it 
I think that’s going to be key. I’m also thinking that the thinner I get them the more likely the cheese is going to get closer to the surface.
Spray the iron liberally with cooking spray before putting the stuffing in. And cook it a bit longer than a normal waffle. I do this for a fun take on chicken and waffles – I do stuffing waffles with fried chicken or pork chops, with gravy instead of syrup. 
This is the kind of thing I’m interested in. I’ve seen pictures of such ‘wonders’ 
I’ve also seen tater tots grilled cheese!!!
https://www.thrillist.com/recipe/nation/tater-tot-waffle-grilled-cheese
https://www.cabotcheese.coop/cheddar-cheese-shake This powdered sharp cheddar is sold in local supermarkets. It’s WAY cheaper than the King Arthur cheddar powder. It adds a really strong cheese flavor to baked items without affecting the texture.
I recall seeing a yeasted waffle recipe on either ATK or Cook’s Country, and remember them saying that, package mix directions notwithstanding, pancake batters do not produce good waffles. The latter need more lift, and should be thicker.
