<img src="http://pictureposter.audiworld.com/37382/batterybox.jpg">

I got some battery vent hose from BMW - 61 21 1 377 745 and I moved the ground connection to the lower nut. It's a little rusty in the battery box. Should I flush it with water and paint it?
<img src="http://pictureposter.audiworld.com/37382/type41battery.jpg">

That type 41 just doesn't fit without more cutting of some upper hold downs at the sides. I can't use the battery hold down piece that worked well with my volvo battery last week. So now it's vented but not secured.

I'd flush the area (and box) with a water/baking soda solution first. That will neutralize any acid that is lurking.

Once it's neutralized, then use an etch primer, then normal paint. That's what I'm planning to do with mine once it warms up enough here.

Once the battery box is clean and painted, you can either use one of the battery mats (Griot's Garage and others have them) or a coating to protect it. I've used Eastwood's battery tray coating on other cars, but it's closer to undercoating than normal paint.<ul><li><a href="http://forum.eastwoodco.com/showthread.php?t=2729">Eastwood recommended battery tray prep</a></li></ul>

<center><img src="http://i29.photobucket.com/albums/c295/rcougle/DSC03828.jpg"></center><p>except that alot of the area around the batt compartment was rusty as well. i hit it with a rust stripper wheel on my drill then primered it up.

As UrScubed suggested, use the baking soda water trick to get rid of any acids. Then clean, sand, and try this product. It really will stop any future issues. Just make sure you prep well. One can will last you about 400 years, so if you have any friends in your area with the same issue on another car see if they want to share it.<ul><li><a href="http://www.aircraftspruce.com/catalog/cspages/acidproofpaint.php">http://www.aircraftspruce.com/catalog/cspages/acidproofpaint.php</a</li></ul>

I think POR-15 makes a pretty well respected product too. I think POR might be more expensive though.