Mystery misfire PLEASE HELP

Hi everybody I'm Sam. Long time reader and I've learned a ton already from TW.
Background info: 2004 Tacoma 4x4 3.4 with 160,000 miles. About a week ago I took it out to the desert and had some fun, nothing too crazy, its my baby. On the ride home I noticed the revs were randomly dropping on the highway, and at stop signs it would really drop and sometimes almost stall. CEL came on.
I put a code reader on it and got p0303,p0306, and p0351 ( misfire in cylinder 3 & 6 and ignition coil A. So I replaced the cool but the problem persisted. New code was for faulty ignition coil wiring. Replaced the other two coils, all plugs and all new wiring with Denso parts.
sometimes it will drive just fine, other days it will misfire badly at about 2000 Rpm's on the highway, at a stop light, or just normal driving.
The p0351 code is still there even though it's a brand new coil.
Any ideas???

 

not knowing your tech experience / level ... the CEL / Codes are not self clearing.

I had a similar issue with the IGN A code and what I discovered was the negative cable pinch bolt had broken and the ground cable was loose. I started to check all of the other grounds and discovered that there was no chassis to battery ground or chassis to engine ground. Repaired those, cleared the codes and so far so good.

 

Thank you for replying! I should have been more clear, it still misfires and runs rough. It's not just the code.

 

SOLVED:
There was a short in the wiring that led to the ignition coils. WHEWW!

P.s. Denso plugs

 

What was causing the short - was it easy to spot or did you have to use a multimeter?

 

I have an aftermarket K&N intake installed before I bought the truck, and it looks like they didn't zip tie the wire bundle leading to the coils. There was a section that rubbed on some metal and frayed through right there.
An auto electrician found it and took care of it. I have such a difficult time understanding electronic stuff