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A barrel filter is only good for about 600 gallons so you will need 6 of them for a 3000 gallon pond. That's OK but you're running into minor balance/distribution problems. You can probably get away with two mechanical barrells feeding 3 bio-barrels but a 3/6 arrangement with each mechanical barrell feeding two bios is better.
2" lines to each mechanical filter if you're using gravity to feed the mechanicals or 1 1/4 if you pump water to the filter. 2" lines between the mechanicals to the bios since the mechanical will have to be feeding two barrels.
You can run the connecting lines into the top of the bio barrels and operate the bios as down flow. The PVC is large enough you won't have to worry about the media plugging up.
Shaved PVC would work well for either mechanical or bio if you can get it or make it on a lathe. If that's a problem, you can cut up 1" PVC pipe into 1/2 to 1" lengths and use that. you will have to clean the mechanical filters often to achieve a high ORP so an open mesh nylon bag isn't a bad idea that will allow you to remove the media, clean it and replace it without a shovel. (You should clean the mechanical filters several times a week.
Rocks are definately out.
Oh yeah, don't get too many fish the first year unless you want to be able to tell the story all of us get to tell about how we killed off so many koi when we started. When you get a sick fish, come back here to find out how to save it but don't give up, we all had to go through a learning curve to learn to do what the older folks had been telling us all along.
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