as Evan has suggested, possibly it is some phantom connections and non-connections. since things have worked sometimes - it is pointing to construction issues - yes I had a few on my own v4 - and yes I have that case type.
I am thinking place it aside until you are patient - then some patient disassembly and inspection with a magnifier and DVM (power off on the rig!). do careful mark which cable goes where AND orientation of each cable.
there is a cool rig there - and I am thinking it may still be undamaged. the finals are cheap - but let's not smoke them unnecessarily. a dummy load that can handle about 10 watts is very useful. without one of those - be very careful to insure rig isn't going into transmit.
with everything on receive seeming to work now except the encoder - it may be an intermittent connection issue there - and that board that Evan mentioned is quite subject to poor solder connects the way it is constructed. proceed patiently and try to learn at the same time.
73 Curt wb8yyy