Has the function of the secondaries been tested? I suspect they are not opening smoothly and fully. This can cause a rich condition for lack of air to mix with the fuel. Also the injectors may have been compromised by the coolant that filled the 2 secondaries. The following is an article on Marc Hiebeck's website.
http://www.zr1specialist.com/HAT%20W...%20Working.pdf
Also the plug wires and the coils need to be tested. Just because their new doesn't mean they're good. I believe a plenum pull shall be necessary to fully test and diagnose.
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