Well, for the tapped holes I would use the harder filler rod. Harley cases are a magnesium alloy very similar to 6061 (a365 I think is the number). So any of the filler rods that work with 6061 will bind just fine with the cases.
for the transmission ears and things like that I'll use 4043 because it's a softer filler rod, and since the mount ears are going to be put through lots of vibration and torque pressures, it's always a good bet to give up a little tensile strength to gain a lot of ductility and elasticity. The softer welds will resist cracking a lot better.

I have to agree that heli-coils and studs are a beautiful thing. Whenever I rebuild an old engine I put studs in all those cover plate bolts. It will help keep any ham-fisted mechanics from ruining your work down the road!

However you decide to weld up the bolt holes, the gasket surface will need to be lapped/machined to a true flat again. Otherwise you'll get leaks and drips, even if you did everything else perfect.