Yeah, pretty much every used Engine runs like new when it is being sold...
So you took the Coils from 2, 4, and 6, and put them on 1, 3, and 5, and the Motor ran on 1, 3, and 5?
If so, that shows the Problem on 2, 4, and 6 is Upstream of the Coils.
Have you checked for Spark using an Adjustable Spark Tester? All Cylinders should have a Spark strong enough to jump a 3/8" Gap
View attachment 416409
If some don't have spark, you could have a Damaged/Shorted Wire going to the Switchbox, or the Switchbox is bad.
Here is a Link to a Ignition System Service Guide
Practical Outboard Ignition Troubleshooting Guide | CDI Electronics - 8th Edition | Detailed reference manual that includes troubleshooting tips, reference data for troubleshooting outboard ignitions,
issuu.com