Alright, enough with the talk of pitchforks and torches and Bangkok surprises.
Foley has been pretty active since Dust got connected to TQ, and he's always asked questions when he doesn't know or understand something, and on top of that he does acknowledge responses given whether they affirm or contradict what he expects to be the answer. Be nice.
That out of the way: I personally agree with the notion that a first-gen soldier is probably a poor starting point for the reasons given by others here. If you spend some time reading up on the origins and history of the clone soldiers (not just via the wiki and Templar One, but also through all of the Dust 514 and EVE chronicles that touch on it) you should be able to find a lot of information to work with.
You don't have to do away with the 'failed prototype' concept, though. I'm sure that the second-gen soldiers with the non-sleeper-origin implants also have their own run of issues that may or may not have left lingering effects on the soldiers even as they moved into clones with 'fixed' implants.
Anslo raises a good point, too - if you can catch Schere sometime you should talk to her; she not only likes neuroscience stuff in EVE and does a lot of stuff with it with her own character, but she also likes helping other people work related things into their own stuff.