The manual can be downloaded from a link on the forum. Go to the Motorhome Tech Topic section of the forum. The sticky at the top has a link to the manual.
On your house batteries not charging off the alternator. Simple thing first -- do you have the USE/STORE switch in USE when you are driving down the road. House batteries will only charge with the switch in USE. If that's not it you might have a bad Trombetta Isolation relay). You'll find that discussed in the manual. Lastly your house batteries may be bad -- although you said they charge off shore power. Don't think it's a ground on the alternator because your chassis battery is charging.