From the Wilwood site troubleshooting matrix:
HAVE TO PUSH TOO HARD ON PEDAL
Too large of a master cylinder. See master cylinder web page to select the correct size unit for your application.
Not enough pedal ratio. Increase pedal ratio, see pedal technical tips.
Pedal mounted at bad angle. Master cylinder push rod should not be off more than 5° in any angle
Wrong pad material for your applications. Pads must match rotor operating temperature range. See brake pad web page.
Frozen pistons in calipers. Rebuild calipers.
Wilwood Disc Brakes - Tech Troubleshooting
Although it seems strange the 1st thing to look for on the T/S list "Too large a master cylinder". The OP did mention going from a single to twin 3/4" masters.
From the How to select page:
Wilwood Disc Brakes - Frequently Asked Questions (FAQs)
Q: What master cylinder bore size do I need?
A:
The master cylinder bore size that you need is dependent on several variables. Choosing a master cylinder bore size begins with defining how the master cylinder will be actuated, manually or with the assistance of a booster, either hydraulic or vacuum operated. Once you have decided on how the master cylinder will be actuated, the information below can be used as a guideline for selecting the right master cylinder. Keep in mind that auto manufacturers have put many years of experience and a lot of testing into determining the right combination for a given car. When building a custom car with changes to the suspension, brakes, tires, and weight balance; you too may need to do some testing to determine which master cylinder is right for your vehicle.
The combined piston area and piston volume of your calipers and the pedal ratio, are two of the primary considerations. Whether the system is boosted or not is another consideration.
Remember that a larger master cylinder bore produces more volume and a smaller master cylinder bore produces more pressure. To determine the appropriate master cylinder bore for your specific application, review Wilwood's Tech Tip Guide. You can also contact a Wilwood Sales Technician at 805-388-1188 or email Sales/Tech Support.
Q: What master cylinder is best suited for my application?
A:
The goal is to select a master cylinder system that supplies sufficient fluid volume to provide a firm, responsive pedal, while generating enough pressure to stop the car comfortably. There are two types of master cylinders, single reservoir, single outlet master cylinders and dual reservoir, dual outlet (tandem) master cylinders. A tandem master cylinder will have two fluid output ports, one for the front brakes and one for the rear. A single fluid output master cylinder, or "fruitjar," will be plumbed to all four calipers as a single system.
Dual master cylinder pedal systems are used extensively in racecars and have completely separate master cylinder systems for the front and rear brakes. This setup permits easy adjustment of front to rear brake bias with the integrated balance bar assembly.
To determine the appropriate master cylinder and hydra-mechanical combination, review Wilwood's Tech Tip Guide. You can also contact a Wilwood Sales Technician at 805-388-1188 or email Sales/Tech Support.