sounds like you have covered nearly all the bases check the float level in the carb and the accelerator pump. The "almost" stumbling could be as simple as a too lean mixture. a quick test would be to contrive to close the choke just a little .... say with a bit of wire..... and see if the engine runs better.
If the engine has been rebored, the increased displacement could be demanding just a little more fuel. The accelerator pump can be enriched by moving the link to the outermost hole on the lever. also, the jet may need cleaning... a welding tip cleaner will work.... remove the tapered soft plug which is just below the lid on the engine side. A pair of diagonal wire cutters can be used to tease it out of its hole. If your engine is not broken in yet, it will continue to improve with use, up to about 2500 miles. Re tighten the head bolts soon. 65 to 70 ft lbs . start with the bolt in the middle between 3 and 4 . a tightening sequence can be found in the shop manual or in a Motors manual.
I got my first 50 in 1965 and have never been without one.