99 Sunfire GT 2.4 Engine

My Son bought this car about a month ago. Now the engine is definately knocking. This car is not worth a rebuilt engine (3700 bucks). Are these engines commonly failing? Are there certain things to watch out for with these engines? I guess we need to look for a used engine. Just hope we dont buy another boat anchor. Another question. This car is a manual transmission. Does the engine have to come from a manual transmission car? Does it matter?