(I just read Matt's response to Mike. I'm still going to post this, but then respond to Matt's comment in a separate post)
The reinforcement around that LE notch does look like it's more cosmetic than anything else (sorry, Matt). And it looks like the cracks are right around where the sheeting meets the reinforcement.
I agree with Mike that some inner structure would have been better -- butted joints just don't have much strength. I would line the inside of such a notch the way Mike did. In fact, I would probably double up the sheet around the notch, then put in the backing plate and the 1/2-ribs. I may even go so far as to double up the sheet with 1/64" or 1/32" plywood to beef up the stress risers at the corners of the notches -- one the one hand I'm a recovering RC guy, so maybe that's extreme, but on the other hand you could make the half-ribs from 1/8 or 3/32 balsa, make up the weight in strategically placed plywood bits, and probably have a stronger model for it.
The reason is that that sheeting is a stressed member of the airframe -- a D-tube like that is stiff because the sheeting is resisting shear forces. If you go and whack a big hole in the sheeting then that nice square hole is going to want to go diamond-shaped when you stress the wing in twist. It'll want to pull at (for instance) the top left & bottom right corners of the hole, and push at the other two. Since balsa isn't very strong across the grain, if you exert enough of that sort of twist on the wing then those box sides will just pull apart, or the butt joint will fail, and that'll be all she wrote.
Putting in half ribs back to the spar will force all of the shear to be in the remaining hole -- the piece that you fill the hole with then essentially becomes a shear web, preventing the hole from distorting. The shear forces will still be concentrated at the corners of the cut-out in the sheeting, which is why I would be inclined to beef up that area with something, but just using Mike's method is probably sufficient unless your name is "Sir Crashalot, Knight of the Ragged Table".
Such a structure as you have may well crack out just from normal engine vibration or from normal flight loads, and it might be limited to just the cut-out and its reinforcement. If that were the case it may well show the "creaks when pull tested" symptom that you're experiencing. If that's all true, then a careful inspection should show two things: one, the cracks are limited to the splices in the fuselage and the box that you lined the notch with, and two, the cracks do not move when you flex the airframe "straight", but do when you twist the wings. So if you're lucky that's all it is.
If you can twist the wings and see the sides of the cracks trying to move against one another, then you done messed up when you made that notch, and you need the "Mike fix". If you can put stress on the airframe "straight" and see the cracks open or close, then chances are that the sheeting is bearing more than its fair share of the strain because something inside is broken. If it's the former then you need to get in there and rebuild the box. If it's the latter, then you need to fix whatever is broke, and rebuild the box. In either case, you probably need to rebuild the box, and when you have the box ripped out of there, you'll have a dandy inspection hole.
Note that if you're really lucky you'll be able to finesse the whole thing, and approach the whole job from inside the fuselage. If that's the case then when you're done the only part of the finish that'll be ruined from your work won't be visible with cowling and pipe cover in place, and you'll still have a nice-looking airplane to fly. It'll require a lot of fiddly work, but it may be less effort in the end than tearing up all that nice paint.