I have recently started using Slic3r 1.2.9 on my Mendel90, and I am pleased with the simplified UI and the fact that it is more regularly updated than Skeinforge. I have come across the Prusa edition of Slic3r and am considering downloading it to use on the Mendel90.

Are there any immediate changes, recommendations, warnings, etc. that I should know beforehand about using the Prusa edition of Slic3r for my Mendel90?

Nothing. It works like a charm. It has more options but these are so intuitive.

If you are using the ooze free start g-code you can use temperature placeholder variables so you do not have to change it in the g-code every time.
Other Slic3r placeholder variables listed here.

M104 S[first_layer_temperature]; set extruder temp
M190 S[bed_temperature] ; set bed temp & wait
M109 S[first_layer_temperature] ; wait for extruder temp

Could you copy me your config file? I have a standard Mendel90 (Dibond) that I've recently got out my attic and I can't find the USB thumb drive with all the software on