I have a 2004 Pilot that started throwing random misofire codes starting with P0301, P0304, P0300 and P1399. It was running fine at the time. We adjusted the vales and cleaned the egr, but the codes still kept activating. The car then starting running rough. Took it in to the shop and the mechanic stated the head gasket was blown. (The car never overheated) We had a new motor installed. (used) Ran fine for about 100 miles then the codes started again. Everything that has been done is as follows:

Adjusted valves
Cleaned EGR
Cleaned fuel injectors
changed computer
changed computer for traction control
changed some of coils
replaced spark plugs

Still throwing codes. Can be from a P1399 only to all codes P0301 - P0306, P0300 and P1399.

Anyone have any ideas? We don't know what else to do. Please help.