UPDATE:
So, my main reason for posting was the implication in jetty's remarks that I may have corrupted my toolhead offsets as shown in EEPROM and had no idea how to figure out what they should really be.
I decided to forge ahead using the standard instructions assuming those offsets are correct.
The Makerbot instructions went OK in terms of a successful upgrade to sailfish (I even managed the reset/hit enter maneuver on the first try ;0).
The only area I had issues was in setting acceleration values, since not all the parameter names in the makerbot instructions matched what I was seeing in RepG settings. So, I did my best to match them and hoped for the best.
My next problem was trying to get slic3r in the 3D toolchain, hoping it would produce better support options. I never got slic3r GCode to work right with RepG, so I am now trying a post-processing Perl script to generate the x3g file directly from slic3r GCode skipping RepG. Some things liked about hat option:
1. The ability to insert start and end GCode
2. Change the way the pre-print nozzle clearing movements work
3. Control initial layer (raft/support brim) thickness, nozzle speed, platform temp
So far, the prints are starting way off the rear right instead of centered, although it looks centered in Slic3r, so obviously some settings to look into there.
None of my other printing attempts with RepG 40/RepG40sailfish have come out, mostly due to first layer adhesion issues (filament balls up on the nozzle).
Dan