I purchased John Watson's Aluminum Extruder Upgrade (http://www.wotz101.com/wotzbotz/index.html) in the hopes of resolving all of my extrusion issues. After receiving the upgrade, I was pleased with its simplicity and utility however, the skipped steps problem didn't immediately disappear.
Upon closer inspection, I was noticing that the filament was constantly getting pulled off of the drive gear by some unknown force (and still unknown, may be a characteristic of my particular printer, not sure). I was not able to see this with the other extruder mods I had, so having the even more minimalistic extruder helped out a lot!
In order to remedy the issue, I decided to create a filament guide which is compatible with the aluminum extruder mod. After installing this mod, I haven't skipped a step yet!
NOTE: I have only tested this on my Replicator 1 Dual (MK7 extruders) and cannot guarantee that it will fit on an MK8+ extruder.
Material: ABS preferred but mine is PLA (I didn't have any ABS on-hand but due to the temperature of this zone I would highly recommend ABS!)
Layer Height: 0.2mm
Extra Perimeters: 1
Step 1: Print off the guides for your printer, a plated STL is available for dual extruder Rep1s.
Step 2: Remove the fans/heatsinks from the extruder assembly and place the printed parts as shown in the photo. It should be a loose fit so that it doesn't interfere with extrusion. The pressure of the heatsink against the motor will keep it in place when you screw it all back together.
Step 3: Re-assemble the fans and screw them onto the extruder assemble.
Step 4: Re-load filament and print on!