1999 Ford F-250 chattering transmission

I have a Ford 250 super duty with a 5 speed manual transmission and a 5.4 engine. The problem is in the transmission and it is noisy in most all gears but especially in 3-5 as you increase rpms. It makes a chattering noise and is gradually getting noiser but when you put your ear on the shifter it does not seem to be coming from it although it is coming from the trasnsmission area. It used to be that if you let off the gas if would stop and start as you accelerated again but now it tries to do it even though you let off but just not as much. Is this a bearing? The universal joints are tight. The truck has 95000 miles on it.