It's possible you might be able to use the existing heat cycling logic already onboard the Zymatic but otherwise you'd also need to get your flow rate correct and/or be able to modulate power delivery to the heating element to prevent scorching.
Hmm that's not a terrible idea on the HEX upgrade. Where'd you find the 12 plate with those dimens?
It looks to me like these are the pumps here? At $30 a pop might not that bad to replace every few years. Have you tried contacting SeaFlo to see if they offer replacement diaphragms?
The Blichmann is 10" H x 6.5" W. Assuming the coil efficiency is comparable to the stock plate based HEX unless you plan on running it externally there's not enough clearance in the lower Zymatic case to fit.