As for the springs, what you have chosen is exactly the setup I put in mine and it works fine. I used the light blue on the top of the 1-2 piston (goes in bore first), and the purple on the bottom (goes in last after the piston). No springs are used at all on the 2-3 piston.
FWIW, here is a list of the springs in order of stiffness and the stock applications:
F7AZ-7F284-CA Dark Blue (94) (Grand Marquis, Crown Vic)
F7AZ-7F284-AA White (95-97) (Grand Marquis, Crown Vic, Tbird/Cougar, Mustang)
F75Z-7F284-AA Light Blue (98-00) (Mustang, 4v MarkVIII)
1W7Z-7F284-AA Light Green (01-05) (Trucks, SUV's, Vans)
F75Z-7F284-BA Brown (Ford trucks & vans, very stiff)
As for the holes in the plate, make sure they are drilled smooth/cleanly with NO burrs. Here is the hole sizes for up to 300hp which should be fine for you (I noticed you chose the higher hp settings and put in some notes):
Hole #1: .160" / drill size #20 ALL APPLICATIONS (you have no change - is yours already that big?)
Hole #2: .081" / drill size #46 (you have .100" which will just be firmer 1-2 shift - ask Darrin or Alan)
Hole #3: .180" / drill size #15 (you have correct)
Hole #4: .081" / drill size #46 (same as #2, but 2-3 shift)
Hole #5: .081" / drill size #46 (you have correct)
Hole #6: .125" / drill size 1/8" (you have correct)
Hole #7: .125" / drill size 1/8" (you have correct)
Hole #8: No Change (you have correct)
Hole #9: .081" / drill size #46 (3-4, 4-3 shifts you have .089 which is ok)
Hole #10: .076" / drill size #48 (you have correct - this is just faster reverse engagement)
Hole #11: .081" / drill size #46 (you have .089 same as #9 which is ok)
Slot opening: I didn't change this, do what RobertP said.
According to Jerry, if you put in a mechanical diode, you can open up #6 to a slot as well - use the slot in the gasket as a template.
There are other Sonnax parts that can be changed, ask Darrin - he knows. I am no expert, but he pretty much is