Looks like I've accumulated some acid in the battery tray, possibly from my charger.

What is the proper way to neutralize this and what steps should I use to paint the tray after it is cleaned?

To neutralize the acid use a mixture of baking soda and water mixed into a very thin runny paste then flush with water. I'm not to sure what type of paint to use so I will let someone comment on that

My battery tray had a little of this problem.

I removed the battery tray from my 41, I used the formula mentioned.

Then sand blasted the tray & hold down, did a bit of sanding and sprayed 2 coats "rust encapsulator” from eastwood. After that dried I sprayed on 2 coats of eastwood's “chassis black” semi-gloss. Which is a good under hood color and sheen.

I also took the time to “clean” & sand” the firewall & frame area’s under the battery tray. After 3 years it still looks great.

Enjoy,
Michael41