Hi, 

That's a lot of work you've put into the humble 142 there. It prompted me to have a look what needs doing on mine still.

I've attached a couple of pictures, on my early DCC conversions I had the same problem as you, as the decoders were too big so are visible inside, though at least partly hidden by the toilet window - to which I added a white sticky label on the inside to make it more opaque. 

I ran the wires between the cars below the floor, as can be seen in the first pic. To some I've added gangways, which are just pieces of thin black plastic scored vertically and curved to fit in the gangway space. They more or less hold themselves in place as they try to spring flat again, but are secured with a dab of glue. They aren't perfect but fill the gap, I wonder if you might be able to use something similar with the wires passing through the coach end, down inside the gangway, and back up inside the other.

(The middle unit above was bought second hand, I think it's a non-runner, but I still need to do something about the red decoder sleeve visible, it'll probably be made unpowered to make a permanent 4-car set)

I also opened up the rectangular hole under the coupling on the cab ends, and to some have fitted BSI couplings and NRN aerials from class 153s that were used as donors for another project.

I only noticed the cobweb on the Regional Railways unit after I uploaded the pictures....!  I think next I need to look at sorting out the livery on that one, as the excessive yellow has always bugged me, it shouldn't wrap around the sides but I assume was a compromise to match the mouldings.