This is not a question of headers too big or too small. I would start fresh instead of guessing. Check the vibration damper to see if it is damaged and check TDC. Then check the cam timing and start at TDC no advance or retard. Check the compression in all the cylinders. Check that the distributor is working properly. If it still has points install new ones and set the gap to the manufacturer's setting. Check if the base plate is moving correctly and the advance springs are not broken. In fact, have the advance curve checked on a distributor stand (yes, they still make them) Are the spark plugs of the proper heat range? How do they look after a few runs on the dyno(the dyno guy should be able to determine that) are they gapped properly? Adding a spacer to the carburetor may make a difference but you still have a major issue. BTW did you keep the same rod/stroke ratio? And I emphasize ratio not necessarily length. I have a rod stroke ratio calculator you could have. Look at my website APPLIEDSPEED.com Race Engine Rod Stroke Ratio Calculator