Yes I agree, the original Decoder fitted into the Troughline Stereo model (aka Mk. III) is very poor, and I am sure responsible for the wooly bass.
I had intended to replace it with one using a Motorola chip, but never got around to it.
The only advice I can offer is to have your second Mk.II looked at by a competant service engineer. There are one or two Members here who have the neccessary knowledge (and perhaps also the required test gear). The alignment notes for the Leak Troughline tuners can be found here:
http://44bx.com/leak/TLalign.html