I agree on rebuilding the carbs w/ mikuni kits. Also, those grey fuel lines have got to go asap. Ethanol breaks them down and spreads this molasses substance all through the fuel system.
Your original problem sure sounds like it overheated. That beeper sounds only when your head gets hot enough to set off that overheat buzzer. Have you checked your cooling system? I would make sure that drain line off the T-fitting behind the jugs is clear. I had mine filled with sand once. Make sure you can bend it at the lowest point to verify no sand blockage. What failed on the previous motor? What did the pistons look like? You need to determine why your previous motor failed before running your new one. Those oiling pumps were pretty reliable. Unless you had an oiler line break, that would not be my prime suspect. If you're not going to use the oil pump, I would take out the oil pump drive shaft to stop it from spinning the pump (if you left it on and didn't just buy a block-off plate). You don't want to spin that thing dry. Those pumps can also be tested with a drill. There is a spec in the manual for how much they're supposed to flow at a certain RPM. I believe the flow has a linear progression, so you can measure it based on your drill speed and calculate what it should be based on the spec.