I'm sure you have but did you do a BLT?

There could be an issue with the tune now that youve fixed the fuel issues, after an engine rebuild there will be a difference in compression and vacuum due to the new parts, your old tune was smoothed out to another engine basicly (as far as the ecu thinks)

My tune was perfect for my engine before it went in for a rebuild but the ecu was tuned around cracked valves and a blown HG, when I finally get the engine back it would be in my best interest to go over the tune from the start and make adjustments to dial it in for the new conditions.