So the low amps seen are from the panel to the controller. You don't know the amps to the battery.
The problem is not simply between controller and battery. Panel voltage should be nearly the same as battery voltage with PWM, which can affect panel amps (IV curve)
Yep, needs a multimeter to check voltage starting with the panel at its pigtails, then each connection. Your first suspect now is where the panel pigtails connect to the "input wires" on the roof. If the panel has a junction box on the back instead of pigtails, that is a problem how to get at it now it is mounted.
If the panel voltage as seen at the input to the controller is ok, then you don't have to check at the panel, which saves a lot of trouble. Still need to find those missing amps though.
1. 1991 Oakland 28DB Class C
on Ford E350-460-7.5 Gas EFI
Photo in Profile
2. 1991 Bighorn 9.5ft Truck Camper on 2003 Chev 2500HD 6.0 Gas
See Profile for Electronic set-ups for 1. and 2.