RT

so you said after a couple days stuff stopped working after you charged the batteries.  was that relying on just batteries?  what kind of refrigerator is there in that, and was it on?  what are you using power wise? as in are lights led, inverter (if using inverter is the battery charger/converter shut off so it isn't trying to recharge the battery off of battery power? )

 what kind of batteries are they (capacity in AH and how many) depending what was running over the two days it is very possible that is normal.  if you trying to charge them in the rv with what ever loads are running then the charger might not have enough output to do the loads and charge the battery so there is that, but why wouldn't you just plug the coach in and let the converter charge the batteries instead of a separate charger?  or use the generator that you had the Auto transfer switch fixed so it would work? 

Last question. when you said

Applied a charger to the 2 batteries and after all night, still won't fully charge batteries

How are you determining the batteries won't fully charge? Is that from a multimeter check at the batteries themselves? Or is that from the push button four light panel in the coach? I ask because I know in my trailer the little push button four light panel only ever shows 3/4 full even when the batteries are fully charged. The only way to know for sure is to take voltage readings straight from the batteries.

Here's a chart of battery voltages. If you notice it doesn't take much for a battery to be dead. That's why it's important to get voltage numbers for us to be able to help you troubleshoot. 

Also when you said

Gen started and had coach electric. Used steps a few times total (literally) and after couple of days opened door and steps wouldn't engage. 

When the steps opened for a couple of days was that with generator off and no shore power hooked up? If so then you know that the house batteries were at least initially charged. 

If your batteries were initially charged then be aware that the house batteries will only have enough power to run the systems for a few days. If you run the heater at night you can pretty much bet on the rule of thumb of "one night per battery" before the batteries are drained and can't power the house. 

A few questions to hopefully help us understand your system and what you have already attempted.

You said 

 Put new batteries in and rv service installed new transfer switch. 

 Assuming when you said "Put new batteries in"  you were referring to new house batteries and not the coach batteries. With the new batteries installed did the interior items like water pump and overhead lights work without the generator running or the RV plugged in to shore power?  

Do you have a digital multimeter to be able to check the voltage of the house batteries? If so what is the voltage with the generator off and shore power disconnected and with the generator running?

Do you know that the toggle switch works and lets power through to the coach? I'm assuming if you flip the toggle switch with the generator running you would know if the switch cuts power or not. 

Yes, a "toggle" switch on the left just inside the door.

Is there a master switch just inside the door that turns off all battery power?