Of cause you ahve checked all the connections in the ignition system.
Sounds like a loose connection somewhere.
While the car was giving you hard a time, did you check if there was a spark at the plugs?
How old is your ignition coil?
I found one of the terminals on my coil to be loose when I had my Throttlebodies fitted... It had run fine.. but surely it was going to cause trouble at some point.