Bosch 009 Pertronix tuning, Looking for advice to get the car running again Options

[Chaznaster]

Hi All. I was working towards getting on the road formally this spring and seem to have caused a problem while digging around the engine bay.
It's a 74 1.8 with a single Weber progressive and an 009 distributor (I know nobody likes that setup ...) and Pertronix Ignitor. We have had it running (adjusted valves and timed it) and even put a few miles on it over the last few weeks.
Today, out of interest and while trying to find out my Pertronix model number, I took the cap off the dizzy, pulled the rotor and magnetic sleeve and took out the Pertronix. There was no part number (ugh).
I put it all back together (it has been running, albeit not well).
When starting, I got a bright flash above the engine (!) and the car tried to run but it will not idle and backfires like crazy. So much so that I am not comfortable trying to start it again. (IMG:style_emoticons/default/confused24.gif)
I did check all the wires and plugs and all seems OK.
I think the Pertronix is still working (it does fire). Could removing and replacing that part mess with timing or hurt the unit itself? I cannot see why but it is running like the timing is waaayyyy off.
Does anyone here have any ideas on what I might have done to cause it to not run well. How about ideas of what I might do to get back on track?
My only thought is to go back to points, static time it to start and go from there ...
I really appreciate the help!