I started with an original Bachmann Spectrum 44-tonner (2-motor version).
I removed the shell by removing the two screws on the bottom that are recessed into the fuel tank. I removed the old Lenz N-scale decoder that I had installed "back in the day" as well as the light board and front and rear lights. I removed the screws that hold the trucks to the chassis and removed both trucks, with their motor and pickup wiring still attached.
The LM-3S was a bit too wide to fit into the shell. I used calipers to measure the shell's inside and outside width and determined the thickness of the plastic shell to be about 2 mm. I needed to remove about 1 mm from each side of the inside of the shell so that the module would sit flat against the underside of the shell.
I used a Dremel with the drum sander attachment and carefully removed enough plastic from each inside wall for the module to fit tightly against the inside of the top of the shell. Since the drum sander couldn't get all the way into the front corner the module doesn't fit completely out of view inside the front of the shell, but other than visually that isn't a problem.
I removed the module from its plastic shell. With an X-Acto knife, I carefully removed the top of the 6-pin socket (exposing the pins) to provide a bit of insurance that the module would fit snugly inside the shell and not interfere with the chassis (the hood slopes down slightly toward the front so there is less height inside at the front than the middle). I plugged in the 6-pin harness, wrapped the module in Kapton tape, and tightly folded the wires back on top of the module (so the wires pass between the top of the module and the inside of the shell) and confirmed that it would fit into the shell.
Now, to make room for the module and the wiring. I determined that I needed to remove about 1/8" of metal (which is about 1/2 the thickness) from the top of the chassis on the front end, which is the end that I decided (arbitrarily) would house the module. With my band saw (24tpi, 1/2" wide metal cutting blade) I cut 1/8" off the top of the chassis, from the front to just short of 1/2 of the length of the chassis, to provide a niche for the module to sit in. I also removed the "nubs" from the top of the rear portion of the chassis to provide more room for wiring (the nubs between which the light board was mounted).
I plugged in the 9-pin harness and temporarily secured the module to the chassis with a small amount of sticky poster mounting gum ("Stik-Tak"). I trimmed back the 4 function wires and the speaker wires from the 6-pin harness, leaving enough length in the speaker wires to connect to a speaker but trimmed the 4 function wires almost all the way back since they will never be used. I trimmed each of the wires from the 9-pin harness as short as possible as I soldered each wire to its respective loco wire. As Bachmann had originally done, I wired the 2 motors in parallel, with the polarity reversed on one motor so both would run in the same direction. I reused the old incandescent bulb for the front headlight since I was able to mount it sideways, nestled into the wiring of the 6-pin harness. I used a 3mm soft white LED with a 1K-ohm resistor for the rear headlight and glued it into the niche that the original headlight was mounted in. I put the loco on the track and verified that the motors and lighting worked correctly. I then aligned the wiring as neatly as possible and taped it down onto the top of the chassis with scotch tape.
There is no room under the shell for a speaker, but I discovered that an iPhone 5 speaker fits nicely under the fuel tank. I routed the speaker wires between the shell and the chassis down to the area of the fuel tank. I adhered the speaker with a small glob of Stik-Tak.
