My name is James and I'm the one you've been primarily talking to about the Direct Y kit and your SD issues. To help with some of your settings, I took a couple minutes to compare and explain the settings that stood out the most. The main issue was that you had settings that some would use for low speed materials like flexibles.
Under Print Settings tab:
Layers and Perimeters
The Solidoodle Z rods aren't metric, so use the following:
0.09878 for .1mm height
0.1976 for .2mm
0.2963 for .3mm
.3951 for .4
And so on.
So start with a 0.1976mm height for you first layar, and use the chart about as a reference. One thing I loved about the SD frames is that I write notes on them with a pencil for time to time, then wipe them off with acetone or MEK. And yes, I had to glance at my frame to write said notes just now 
Under Advanced in the Layers and Perimeters, change the box from Aligned to Random. While this will add peanuts to your print time, it will give you a consistent print without an unsightly seam on one side.
Infill
Density will be your choice, but I get better reliability with infill at or above 40%. Mechanical parts such as carriages, extruders, etc., need to be printed 90-100% infill. Set your fill pattern to Rectilinear as well as your Top/Bottom. This will pick up speed due to the constant pattern.
Speed
Here's my settings, but remeber that I run an E3D v6 with a Volcano. So while these settings hardly push my extruder to the limit, it may be a hair faster than your current stock setup may handle....some users reported 60mm/s as their limit to still gain resolution and fitting parts.
Perimeters: 80 mm/s
Small perimeters: 35 mm/s
External perimeters: 80%
Infill: 75 mm/s
Solid infill: 50 mm/s
Top solid infill: 40 mm/s
Support material: 70 mm/s
Support material interface: 60%
Bridges: 40 mm/s
Gap infill: 20 mm/s
First layer speed: 80%
Advanced
Default extrusion width: 0.48 mm (On the later SD3s, SD switched to .4mm nozzles, so the given .48 allows for 20% expansion. If this starts behaving like it's trying too hard to push the plastic out, change it to 0.42 mm as you may have one of the older .35mm nozzles))
First layer: 0.5 (This will give you a finer first layer expecially with larger layer heights)
Filament Settings:
Filament
Diameter: you will have to accurately measure for this. If you have filament ranging from 1.70-1.75 over a couple yards, then find the average; in this case, 1.73
Extrusion multiplier: This is where every user will have a slightly different number depending on their modifications and calibration. After you have made all necessary changes needed, adjusted your belts, and re-re-re-re-re calibrated your extruder, this number will end up bneing closer to .95-1.0...but again, this will change depending on your machine.
Printer Settings:
Custom g-code
Try these. This is a slightly modified start/stop code I've been running for a few years now.
Start:
G21; set mm units
G28 ;home all axis
M190 S[first_layer_bed_temperature] ; set and wait for bed temp to be reached
M104 S[temperature] ; set extruder temp and start heating
G90; set absolute coordinates
G1 Z5 F300 ;move platform down 5mm
G1 X10 Y18 F3000 ;move to front left corner
M109 S[temperature]; wait for extruder temp to be reached
G1 Z[first_layer_height] F200 ;move platform close to nozzle
G92 E0; reset extrusion distance
G1 E6 ;extrude enchor
End:
G28 X0 Y0 ; home X axis and y axis
M104 S0 ; kill extruder temperature
M140 S0 ; kill bed temperature
M84 ; disable motors
Extruder 1
Nozzle diameter: either .43 or .48 as explained earlier
Speed: 55