OK, start over... 1.) check compression. 2.) check spark 3) drain the gas and use fresh gas.
Now address the crank seals. If the crank seals are bad, it will start hard, not idle right, not pump fuel right, run poorly at top end, etc... Never a bad idea to change them if you don't know how long they have been in there, and sometimes even then. I have seen new seals that have torn or leaked. Especially if engine temp seems to make a difference.
Carbs, the left and right carbs are not identical on the Intruder. they use different jets to compensate for one running a touch warmer than the other. Use Mikuni needle and seats, others tend to leak.
Exhaust. If the exhaust has a mouse nest inside, it could start hard and run erratic.
Fuel pump. There is a check valve on them that can leak, and on the outlet side, there is a screen filter inside the pump. If you rebuild the pump, make sure all the gaskets you replace are the same as the old ones. the one for the check valve has been known to be missing a hole that activates the valve. (been there)