I recently bought a high flow cat (ebay) and found that the end that connects to the down pipe doesn't match up (right connector wrong angle off by like 25 degrees). was wondering if anyone else had this problem and how they fixed it?

Cut it,find the right angle, then weld it...

thats a common problem with "Universial" stuff.
as above said you can either cut it and reweld it, or you have to fab an adapter plate.

would it be better to cut the cat or the down pipe to make this adjustment?

Now, what have we learned about ebay parts? ;)
But, as previously stated, cut and re-weld.

that e-bay parts don't always fit properly. :(
looking at some SS headers now. going to wait on the cutting and welding until i get those in so i know they match up. luckily i have a friend that welds so it shouldn't be a problem.

I have a header from ebay, and before this header was a different ebay header. They both came with the flange at an angle just like the stock exhaust. IMO i wouldnt bother with and ebay converter, which is just a resinated test pipe. In my experience all it did was make my car sound terrible. i would stick with a stock cat or dish out the dough for a real high flow cat.

The downpipe that came with my header also was 45 degrees off...just cut it and reweld it straight. After that, my whole system was able to line up fine, except there was a 3" gap between my "high-flow cat" and downpipe, so I had to fudge it a bit. Maybe it's just my car, but the resonated test pipe I put on didn't make it sounds bad, made it sound better. More of a smoother sound.

so i need to tell my friend thats welding my stuff to put it at a 45 degree angle to match up to stock?

Maybe not 45 degrees. Just cut it and eyeball it to make sure it'll line up.

most accutate way is to cut it off, mount the exhaust set up, and either tack it while its on the car or at least mark the flange and the cat.
then pull it off and weld it up nice