2005 mustang gt missfire

just joined the site a few minutes ago so not sure if I am posting this in the right spot or not but here it goes.
so I have a 2005 mustang gt with 83,000 miles and the following modifications,
frpp hotrod cams
jlt cold air intake
bbk 62mm throttle body
ford racing intake manifold
driveshaft shop aluminum driveshaft
ford racing 4.10 gears
upper and lower control arms
bbk longtube headers
bbk o/r x pipe
3" magnaflow magnapack catback
msd coils
eibach sportline springs
eibach shocks/struts


so here is my list of on going problems I am having I have been getting a check engine light and when I read the dtc it says p0316 for misfire detected on start up first 1000 revolutions, well I only got that code once then I cleared it and have not seen it since. another code that I have that I use to get all the time but recently has not came back is p0340 camshaft position sensor a circuit bank 1. those 2 codes have never came back now my current problem is while im driving in the interstate for a extended period of time above 80 mph my check engine light starts flashing for a misfire im assuming and while it is flashing the car runs very bad starts sputtering and the loss of power is un real but after 10-15 seconds of it flashing it goes away and the car starts driving fine. i replaced the coils thinking that i may have a bad coil but that did not fix my problem so i replaced the fuel filter once again the problem is still here then i went and changed my plugs still nothing. the codes i have now are p0358 ignition coil h primary secondary circuit and
p0302 cylinder 2 misfire. i am stumped, don't know where to go from here. my next guess is maybe replacing the fuel injectors.
also in the morning when i go to drive it it hesitates and sometimes backfires until the car gets completely warmed up. can anyone help me out on this please, any help will be appreciated!