It's really too puzzling. In all my honesty I cannot imagine the exhaust to be the reason of car shaking and coughing, as many people above...[&:]
It is most probably something related to electrical things, not necessarily to ignition, though. Fuel is all electrical nowadays, too.

 

This is probably something I will hate about Hondas forever... I can take my german cars through anything and they NEVER have problems... my civic is ONE OF A KIND!

 

have you checked the alignment? it seems wierd to me that the in/out mods would have anything to do with the car shaking, and it seems more likely that its the alignment making it act strange as it does little mini-hydroplaning in the rain. can you take the exhaust off to test w/o it? and its a shake, right? not a vibration (sound)?

 

It is definetly not alignment... the engine actually sounds like it is drowning... the sound and shaking is coming from the right side and it sounds like a gurgle.

 

dude the only thing I can think of is that it's all in your head with the cai but you say when it rains? it's probably when you brake. check it out next time. maybe your rotors are warped.

 

this thread is friggin oldd man lol