I doubt it has anything directly to do with the alternator. However, check that the fitting of the alternator has not unintentionally disconnected the vacuum line to the distributor, which would affect timing and also give a manifold leak. 
There are other possibilities, but perhaps the most likely is an ignition timing problem, or possibly a partly blocked jet in the carburettor, or even the carburettor flooding. If it is a Zenith, check the mating surfaces of the top cover for flatness.
John
				
			 
			
		 
			
				
			
			
				John
JDNSW
1986 110 County 3.9 diesel
1970 2a 109 2.25 petrol
			
			
		 
	
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