P0301 misfire

Question

I'd love to learn more about this issue. I have a recently purchased 05 Prius with 219kmi. New main Battery 4yrs ago. It has thrown the CEL with codes for misfire on P0301 and P0302. I replaced #1 plug and swapped the #3&4 COP with #1&2, cleared the codes. After 30 minutes, the codes returned, the issue did not move to 3&4 as I expected. The removed plug was clean and brown as expected. I sprayed starting fluid around intake to test for a leak near 1&2 with no positive result.
I Paid to have codes read by a reputable garage who confirmed the codes, tested the injectors-o.k. and declared the wiring harness o.k. Saying to replace the COPs and plugs; maybe have a compression test done.
So, why didn't the problem xfer to 3&4 as expected? with 1&2 still showing misfires I suspect the harness or connectors. I can buy a compression tester and test if needed. Thank you for any info you can provide.

Answer 1

I should have mentioned the main battery was changed with oem 4yrs ago and the12v battery replaced in Aug 2018.