I used have to nice downpipes on my cbr 29 but sold them, I’m now probably putting the standard back on. I have a viper end can which sounded nice and spit flames sometimes, will the engine still run well, or will it be a lot different? Could someone explain a change if any, Thanks

This is depend of the inner diameter of the downpipes and setting you have done before. If you simply put downpipes to stock engine and do not change anything in fuel\air flow - so, there wouldn't be any issue with fitting stock downpipes. If there was any changes to increase air\fuel flow - so, after fitting stock downpipes you can run little bit rich - which is not so bad for the engine, as lean :))) But generally better to adjust carburator to current downpipes.