A bit late for this question, but your post #1 said "I need to replicate the way a magnet is being energized by a controller". Unless I've missed something, it's not clear why? Given that you have accesss to a machine designed to drive the valve, why the precise waveform replication being attempted here? If you simply want to use the valve other than with its original machine, won't a simple peak-and-hold drive (as used for a fuel injector) work for you?

Well, for starts, it's not a valve for a fuel injector. But you have a point. Maybe I shouldn't bother so much in cloning the exact waveform and concentrate rather in controlling with precision its open and closing cycle instead... which is what's really important. It's just that I'd like it to behave as closely as possible to what it's originally been doing. And on the other hand, I've become very curios about how its controlling circuitry is doing what it's doing.
I guess we've reached the point in which the only way to know for sure is to actually build the thing... We'll have to wait and see... Thanks for your input!

EDIT: I think I understand your question now... I'm trying to replicate what the controller is doing because I want to later bypass it and modify the valve's behavior

 

Yeah... I'm not as electro-savyy as you are, but I've noticed that anomaly too... could it be that there's a transistor circuit trying to feed constant current to the coil? Also... if you pay close attention to the mid part of the waveform, the down notches reach almost exactly -7.5V, while the top tends to stabilize at around 5V... could it be that the supply is not 12V ?
Anyway, I've decided to tweak the PCB I've drawn to include the latest changes, and to make it as easy as possible to change components back to the previous version if needed... I'll post a pic of the PCB layout and the complete circuit when I'm done.. which I think could be by this friday. Cheers! and thanks for all your help!

My bet right now is that the 12 volts "sags" so it is not really 12 volts for a while. Maybe you could scope it if you get a chance.
Alec, your right it is much like the fuel injector circuit you posted earlier, except the time to open is tightly controlled as is the holding current. Very little variation with either voltage or resistance of the coil.

 

With an on/off valve I'm struggling to see why you need to tightly control the opening time. I would have thought that in all uses you'd simply want the valve to open in the shortest possible time (hence the high voltage supply, albeit with current-limiting, being necessary)? I can understand that the time the valve stays open, and the reduced current during that period, need to be controlled; also that a negative pulse at the end will speed up the valve closure.
Do you really need to supply those negative blips during the plateau? They can't control the already-open state of the valve.