Not sure if this is helpful in any way, but: I drove the car to work this morning about 45 minutes, 35 miles at about 70 degrees. I checked codes this morning when I got there with the X4 after clearing last night and there were none except P1000 (monitor testing not complete), normal. I stopped on my way home for gas after an hour of driving, but at about 90 degrees outside. In addition to the first code I had P0300 and P0316. I was only able to see this when reading with the X4, no check engine light. I was reading that the misfire codes are two step codes, where they need two or more key cycles for the light to come on. After several key cycles of starting and stopping, no light but the codes remained. This makes no sense to me right now.
I went & checked on the origin of the Ford P0316 DTC code & found that this DTC came about sometime in '06-'07 due to Fed gov demand to start monitoring for
OL cold start emissions (was only monitoring for emissions once PCM was in CL operation prior). Since the PCM is in OL operation due to O2 sensors being inoperable (no signal output) due to low O2 sensor operating temps at
initial startup the PCM is looking at the crankshaft sensor for crankshaft acceleration velocity of individual cylinders to then compare against the other cylinder's acceleration velocities to determine if a cylinder is "out of phase" (most interpret as a misfire, thus emissions due to spewing unburnt fuel into exhaust) during the initial startup up to the 1000 rpm mark (usually when the O2 sensors reach the operating temp they need to start generating a signal to the PCM then the PCM goes into CL operation). As long as the accelerations during this time period are within a certain threshold all is well but if at least 1 cylinder's acceleration falls below a certain threshold
in comparison to the other cylinders accelerations then the PCM will set this DTC. This could also cause the P0300 random misfire DTC to set as well since the PCM has to be in CL (needs the O2 sensor output along w\ the crankshaft sensor output) in order to isolate a misfire to a single cylinder (the P0301, P0302, P0303, etc). Ford vehicles earlier than '06-'07 won't have this P0316 DTC capability unless the PCM firmware has been updated....most likely thru a TSB issue.
The actual cause can be a LOT of things, but 1
known thing in particular in this instance is the distinct cylinder acceleration velocity variations caused by large overlap camshafts which really are more prone to setting off a P0316 code
if the original OEM cold start crankshaft acceleration thresholds (calibrated to the engine cylinder accelerations using the OEM camshafts) in the tune are being used as these camshafts will cause excessive variations in crankshaft accelerations, especially at low engine RPM's (thus the sound most admire) & are very sensitive to outside influences (temp at cold start, fuel quality at cold start, quality of the tuning associated w\ them, etc). This can be fixed in the tune in 3 ways..... 1.) reset the start up crankshaft acceleration offset threshold to more favorably match the acceleration patterns from the cams or, 2.) retune the engine to smooth out the accelerations to bring them back within the OEM thresholds or, 3.) disable this particular P0316 DTC code in the tune so the PCM won't be checking for this during start up as this is strictly due to an emissions requirement during cold startups while the PCM is in OL operation....that is, as long as it is not required to be active in the PCM to pass emissions testing. Once the PCM is in CL & these conditions still exist they'll show up as P0300, P0301, P0302, P0303, etc so you have a decision to make as to which path you want to go down.
When you're checking the codes, check to see if the code is set as a pending code or permanent code (pending codes will not initially set the MIL as more instances are needed for the PCM to determine if issue is a permanent issue....only when the PCM has determined the issue to be a permanent one will the MIL come on). Don't remember if a SCT X4 tuner will read a pending code (I use a hand held scan tool for this as I'm also looking at other items that you can't see using a SCT X4 tuner) so can't reply to that.
I find that it helps to understand the meaning\intention behind a particular DTC code to then compare to known conditions to help w\ diagnosis.
PS--This issue could be as easy to fix by just increasing the engine's idle speed enough to smooth out the engine crankshaft velocity variations caused by these Hot Rod cams...…………..just a thought...………..