certainly use an opto to isolate your controller from the coil, the spikes will wreck it
recheck the resistance of the primary, i suspect 2.3 ohm not 2.3kohm. most modern
car/bike coils are 1-1.6 ohm with the switch (MOSFET, BJT whatever) limiting on state
primary current to 4-8 A.
in Kettering ignition systems the negative going spike is normal, dont panic. if you attempt
to clamp it down or otherwise damp it you wont get a spark. in fact it is that same spike
that gets transformed into the secondary and thence to your plug.
MOSFET's arn't very good in the reverse bias region and can be expensive and time consuming
to get right. Horozontal output trannies from old TV's work. they are just a highvoltage BJT,
old school stuff. they have poor forward current gain though, commonly about 5. be prepared to
amplify big time. high voltage darlington pairs could be the ticket tho...