Dick's pretty much nailed the problem you face. Any vertical adjustment of the BC and leadout exit will have to pretty much be a WAG.
A considerable reduction in any such change would result from hanging the engines horizontally rather than inverted (I'm assuming upright installation is such an ugly thought in never enteredyour mind).
Doing this would remove a huge percentage of the weight normally associated with the fuselage. The configuration you're suggesting would have the lions share of the weight concentrated in the wing itself: engines, tanks, mufflers, spinners, etc. If you take that weight out of the fuselage it becomes little more than a structure to connect the wing and tail. Actual fuselage weight will be minimal and at least part of it will be on the same horizontal plane as the wing and powertrains.
The horizontal stab and elevators will likely be slightly below the wing centerline and will contribute to a lowering of the vertical CG to the extent of what they weigh times their distance below, roughly, the centerline of the wing.
A ball park estimate is that the vertical CG might be lowered by only an inch or so from the normal mid tip airfoil position we generally use. The weight of the landing gear will be contributory as well. With the high wing the gear shouldn't need to be very long and I'd do my best to minimize that dimension as much as possible. If the gear is mounted in the engine nacelle area the entire mounting structure would be located above the vertical CG and will minimize the effects. Only the part of the gear and wheels below the nacelles will impact the vertical CG in any serious degree. Keep the wheels light (Dave Brown foamies, for instance) and you'll minimize the gear/CG issue.
The landing gear will be a primary source of additional problems and they'll have as much to do with the drag associated with it (well below the thrustline) as it will with the weight. I would do everything possible within your design concept to reduce both the weight and size of the gear and wheels for that reason. In a stunt design that will ultimately be a greater issue than the vertical CG reference the leadout location.
A lengthy gear and big wheels will move the vertical center of drag further below the thrustline than conventional layouts. When coupled with the high thrust line you'll have a significant moment between the two which will likely require some trimming in terms of stab elevator incidence. I would definitely not build in any positive incidence in the tail as is now becoming common on generic stunters. The displacement of the thrust line and vertical center of drag will accomplish the same effect by virtue of drag vice lift.
It is possible that ultimate flight trim may well require a bit of up elevator (relative to neutral flaps) to get inside and outside turn rates symmetrical. I would not build in negative incidence[/u] in the tail in anticipation of that, however. Tests have shown any degree of negative incidence (the equivalent of "up" elevator) to be destabilizing-stabilizing in conventional designs. I'd plan on using up elevator as a trim device if that should prove necessary.
Ted