<<1. That pipe I got from pep boys. I cut it so its a perfect fit but its 2.5" when my j-pipe and ic pipe is 2.25". Now being its bigger i put it over both pipes and I am gonna put the silicone hose cover on top of it. Is that bad ? Will that hurt the air flow ?>>
Well, yes. It's kind of like the difference between "press-bent" and "mandrel bent". There will be a lip on the transition on the downstream pipe. You'll want the transition to be as smooth as possible. I would try some t-bolt clamps and crank down on them so that the edge of the smaller pipe is closer. Why didn't you just get the 2.25" flex pipe instead of 2.5"?
<<2. My j-pipe is squeezing my lower radiator hose just a bit. Is that bad ?>>
as long as it's "just a bit", I wouldn't worry too much. Just check on it from time to time to check for wear.
-Tony 98'GST (soon to be neglected) 92'TSI AWD (soon to be modded)