Upgrade an Atlas SW-9 to PS-2 ??

There is not a lot of room inside those Atlas switchers. An MTH body swap probably wouldn't work because I think the MTH switcher body is wider so the PS2 parts will fit. I think your best be would be to use an ERR MiniCommander2. I doubt know where you would get electro couplers though.

Here is what you have to work with. Special bottle neck board and ribbon board to the front for the Sound Power board.  Not a lot of room above these board once the diecast hood assembly is installed.  The original  Dallee to TMCC conversions require a new frame for more room.    8 ohm Speaker is in the fuel tank.  A wafer speaker, very small, you would also have to change here, I believe MTH speakers are 16 ohm. 

Antenna location was an issue, improved on later installs.  MTH  units don't require an antenna, not an issue.   Head/Rear lights and cab light voltages may have to be changed.   Power pick-up from track should be fine.      

Another look.  Note the the single motor double flywheel assembly to the two drive towers takes a good bit of space.   Full cab detail doesn't allow much to the rear.

The biggest problem is "getting" the proto2 boards, unless you've got a stash already!

I'm thinking about the ERR boards for mine and even the lil Beefs and Beep I have...but you probably wouldn't know anything about those engines.....