What about the air cleaner?
These carbs are pretty easy to set up with the stock airbox, filter, and exhaust - assuming the carbs are cleaned well. Open pipes will present tuning issues, not too severe: usually just a main jet change and needle height change. Pods plus open pipes is a serious challenge to tune with decent results!
Mis-adjusted ignition timing can really destroy performance, I would check that first.
You should be able to go highway speed sitting upright on a 350-Four, it will work hard uphill or into a headwind though! I wouldn't go on a cross country trip though: although a 350-Four in good condition would be able to do it I would be in bad shape from the vibration and wind.