Hi all. I purchased my 2006 S-type 3.0L V6 about 10 years ago with 32k miles. I’ve had no problems until last year when it went into limp mode. I found that it was misfiring (I think 2, 3 and 5) I didn’t it much over the winter. I replaced the spark plugs and coils on the driver side. I still had misfires on 3 and 5. I finally got around to replacing the spark plugs and coils on the passenger side. (What a terrible design getting the spark plugs on that passenger side. That’s when the problems started. It started fine but in drive it continued to misfiring on 3 and 5 then 1,3 and 5. Then stated to run rough and stall with multiple codes. It turned to be a bad battery and stated great with the new battery. But started to have multiple fires on 1,3 and 5. P0300 and P0316. I maybe I did something wrong putting it together and took the intake manifold off and reconnected everything again. Now it starts but it’s very rough and stalls out.
The codes now:
P0300
P0303
P0304
P0305
P0306
P0316
P0661
The gaskets around the manifold tuning valves looked good. Connections seem tight.
I don’t know where to go next. I thought just replace the lower manifold tuning valve but now it’s misfiring on 4 and 6. I’m totally bummed.

i would love some guidance. Any help would much appreciated
Dave
2006 Jaguar S-Type 3.0L V6 62K miles