Nice work so far. A couple comments on things you've brought up.
When you grind tabs off the frame, a flexible disc will maintain the radius of the tube more easily than a hard disc. A hard disc can quickly leave flat spots on the frame which are noticeable.
It seems you're going to some serious lengths to customize that machine. If you're considering power improvements, then I really recommend boring the carb throats. The carbs on the 350f are bad choke points, but can be made to flow much more air by a competent machinist. Next up for power improvements on the 350f is the head (ports and possibly larger valves) and then exhaust. Rick Denoon at DenoonSP will work magic on your carbs if you're interested.
For your spark plug threads, I wouldn't recommend a helicoil unless you can find one with a tapered final winding. Otherwise you'll have a gap in the contact between the crush washer on the spark plug and where the end of the helicoil "coil" stops. That gap can be filled by doubling up on crush washers with one larger than the other, but that's a dodgy solution. Timesert makes a good spark plug repair kit that would offer a better sealing surface.
Please post pics of the weld on your tank. I've considered doing that myself, but the cost is prohibitive. It seems a seam welder would be a great way to weld those tanks up (I think that's how the factory did them), but they aren't common.
Camelman