Welcome to the SeeMeCNC Community

Normally we run PLA and ABS on our Orion. We've been getting decent results so far very pleased with both machine and software.

Lately however we've been running nylon and PETG and seeing a lot more pimples than we did with PLA. Any tricks or tips to optimize the retract settings to reduce this to a minimum?

My answer may be a little late, but I found a Retraction Tower Test Tutorial on Thingiverse: http://www.thingiverse.com/thing:2157858
I'd play with the retraction distance and speed at first, and then move on to wipe and coast. I can't personally vouch with for it (yet), I've been having other issues with my printer...fixable but time-consuming.

The best part about the tutorial is that you learn a little more about how to set up your prints to have different processes in S3d.