Mark is spot on.
Setting the base timing on an old school ride a few times will teach you to do the whole job right.
Try dialing in six dueces on a jag v-12, or two fours on tunnel ram bolted to a high compression v-8 (with a bumpy cam), and get back to me on how hard a graaavy lil four cylinder can be!
Back in the day we had weights, springs, and vacuum advance cans as our only tools to make the ignition happen at an appropriate time. (and we were happy /ubbthreads/images/graemlins/tongue.gif )
Hell, when I was a young pup, I had a buddy with a distributor machine, and I spent many a sunday over at his shop playing with the curves. Little more spring little less weight, eventually we get it dialed in so sweet we wanted to call the manufacturer up and tell them they were doing it all wrong... 'till we tried to get it thru emissions, or caught a weather front just wrong, then you'd need earplugs to drive the damn thing... it'd sound like hail on a tin roof... /ubbthreads/images/graemlins/rofl.gif )
With these new fangled electronic engine management systems, you can set it wherever, and then tell the ecu whatever you want about the crank poition.
According to the tOOners, that's just fine...
Reality has it's own ideas though, and as you have just found out, you're starting from scratch every time you make a change.
I mean, for fawks sake you can tell the damn ecu it's the fourth of fawkin July, when it's really December. If you miss the base timing and then build a tune off of that.... If you make any changes and don't calibrate the rest of the tune for that offsett, well you're gonna spend a lot of time on April first...
Set the timing correctly, adjust the biss correctly, and then build a new map.
Just the opinion of an old guy who has "fixed" many a mysterious, unsolvable tOOn problem by going back to basics.