i read something once about the break in of a barrel was basically filling in any voids with copper. my question is can i mess up my break in by cleaning my barrel back to clean steel? i am getting blue on my patch when i run the Bore Scrubber thru it. how would i know when to stop?

There plenty of debate about break in process. I think you are fine. My gun manufacturer suggests cleaning after every shot for first 20then shots.

Also to clean your brushes just use a bore cleaner. Then rinse with water and shake dry. Seems to work for me.

How often you used to clean them? Is it necessary to clean them regularly?

Every time I use the. I clean my brushes about halfway through my cleaning process so I don't keep putting crud back in my barrel.

Kroil is all I use. inside & out for cleaning/oiling.

If you are using a copper solvent the patches will come out blue as you have noticed. But also with the bronze brush which has copper in it will leave a black residue in the bore from the solvent if it is a used brush. I dislike the ammonia based copper solvents for personal reasons. I've found that Hoppe's Elite copper solvent is a good product for removing copper fouling. And with this you can swab the bore and let it set for a while without stinking up the room and giving it time to do its magic.

how much does copper fouling change groupings as compared to a clean bore?

Every barrel is different. I have had rifles that would double the group size when they were badly fouled. On other rifles the groups opened up, but not too bad (rifles with smooth custom barrels). It is usually not a problem on rifles meant for big game hunting.

On medium bore rifles like your .338 it usually is not as much of a problem as it is with the small diameter rifles.

that's what i was wondering. i spent a lot of time and money on ammo thinking if i got all the copper out i would somehow end up with a great shooting rifle. i pulled out my old (40 yrs) 270 and when i cleaned it i discovered it had lots of copper fouling. i had never really done anything but swab it out with basic cleaner. i did clean the copper out and it shot a great group. nice old deer gun that i will never get rid of. i did ship my 338 back to remington yesterday. just couldn't get any consistency in groups. i was shooting anywhere from 2" @ best to 4 or 5". i talked to a guy that does a lot of competition bench rest shooting and he thinks it needs a new barrel. his suggestion was to give remington a shot at it and if that didn't work to go the custom barrel route. here's hoping this works. it's been a fairly long and painful experience to this point in time. i have always shot remingtons and felt they didn't make any bad guns so i tried to fight thru it before sending it back.

Do yourself a big favor when you get it back and bed the action. I have never seen a hard kicking M700 (like your .338) that did not improve with a proper bedding job and a floating barrel. Even if it is only the recoil lug that gets bedded it should make a difference.
A bedding job is $100 project (DIY is a $25 project) - a custom barrel is $600 project.