Like the topic said.... gets worst when you floor it in 2nd 3rd and fourth gear, But runs perfectly fine when the engine is cold.
Would axles cause something like this to happen?

 

What car? What swap? Are you using aftermarket mounts? It's hard to help when we don't know what you have.

 

88 crx si
B18C5
Hasport biLLet mounts

I mean it shouldn't be the motor mounts though cause remember the vibration gets worst when the motor is warm. But when its cold it runs smooth and strong.

 

I have a 91 CRX DX with a 96 B18B1 and I'm also using the HASport billet mounts. They are stiff when it's cold and vibrate a lot but you say your's gets worse after driving for a while? I would check to make sure all of the mounts are torqued in sequence and to the proper specs.

 

check your axles, this happened to me when I had a b16 in my EF. It would only happen while accelerating up to 30 mph or so. I changed my axles and the vibration went away.

 

Check your axles, that could be the root of your problem. If you look at them and dont see any tears, then it may the the innner cv joints giving all the vibrations.