BillH:
How much right thrust and down thrust should be incorporated into the engine mounts?
I would leave the engine thrust line at zero-zero. By raising the prop centers you have added a little effective down thrust, and with the 80" span the offset thrust will not have a great effect with an engine out. What you might do is lengthen the after fuselage by five to ten percent, which will give greater rudder authority and help to balance the increased engine weight also. And one further aerodynamic note: You can never have too much rudder area on a twin.
What sort of added reinforcement should be done to the wing at the engine mounting points? I see tying the engine pylons to the main spar, extending the center sheeting out past the pylons and possibly putting in a diagnonal brace from the pylons to the TE at the wing mounting bolts. What forces are involved with the engines?
My very first twin, the Tiggerkitty, has basswood mounting beams in the wing structure, with bass spars running from the wing main spar forward to the firewall of the nacelle. It is far overbuilt. Great Planes, on the TwinStar, cut the leading edge and sheeting away between two ribs, and glued the nacelle sides to the exposed ribs. From the Tiggerkitty I went to ply formers in the nacelle, extending into the wing structure glued to the leading edge and the main spar. This is the way the C-3/10 was done, you can see a bit of it in the picture showing the pump. From there to only one former going in and glued to the main spar. This is the way Northeast Aerodynamics has the Twin-Air 45 built. My latest designs are the simplest of all. I've adopted Dave Platt's method which I first saw on the Duellist 2/40. It's also the lightest. Sheet the wing normally, being sure of the fit and glue joints to the ribs, then just glue the nacelle sides to the wing sheeting, being sure the sides are aligned with the ribs. I've never done one completely under the wing this way, I've always had the nacell lap over the leading edge to the side opposite to the main attachement for a little added strength. And it looks better, too. You can see the overlap in the attached picture of the Tiggerkitty - it was done there for both scale reasons and appearance, it surely doesn't need the added strength.
Your diagonal brace wouldn't be a bad idea, either.
Bill.