If Manchin was primaried and lost the Democratic nomination I don't know what the results would be in the general election, however, I absolutely think it's worthwhile to primary Manchin, if for no other reason than he's a sleazebag a--hole.
The issues I would go after him with would be his endorsement of Donald Trump in the election (I don't know if he officially endorsed Trump but he didn't endorse Hillary Clinton and he certainly De Facto endorsed Trump.)
This has led to the loss of health care subsidies for West Virginia voters and all for the lie that the historic coal industry can somehow be brought back and the jobs with it.
Senator Manchin decided to play short term politics in 2016 rather than look at the long term, and he should be removed from the U.S Senate if for no other reason than he's too stupid to be a U.S Senator.
Manchin said he voted for Clinton. He just won't admit whether he voted for Obama in 2012 or not.