New battery, new alternator, new alternator pigtail, won't stay running; ideas?

Yes, yes, until the battery is drained. Used engine 5,000 miles. Check charge system message has been on since initial start up after engine replacement.

Simply put, your charging system is not functioning. Ensure your belt is installed properly as per the diagram that shows routing. Check for any blown fuses or faulty relays related to the charging system. Check each wiring connection - cabling for both positive and negative sides of the battery. Something is going on that must have changed between the old engine coming out and the new one going in; must be related to the activity around that action.