Can't figure out a misfire issue
 

Just hoping someone can help out...

I have a 2004 3.0 AVK. rebuilt the entire engine due to sludge about 2 years or 50,000 km ago (brand new heads and re-man'd bottom complete with complete t belt job and new slave cylinder but left in the original clutch) car currently has about 325,000 km on it.

so a few weeks ago I started up the car and it started to misfire, didn't throw any codes but after a few seconds it normalized. didn't notice anything at that point and it drove normally. a few days after i started it up again and the misfire came back. it did throw codes at this point and i took it to the mechanics. If my memory serves me correctly, it threw misfire on cylinders 2,4,5 and 6. And a random misfire code. The fuel pump had been making some noise for a while and since 2, 4, and 6 are on bank 2, furthest from the pump, we figured it may be a fuel issue and replaced the fuel pump and fuel filter.

Same problem persisted... its no longer throwing any codes

we checked vaccuum, mechanic said it was all normal, plus could not "hear" any leaks. he pulled all the coils and plugs and all looked to be well. our next step is to replace all 6 plugs, and buy an extra coil move it around to see if its a bad coil.

now on top of this, today i'm having a problem with the transmission. it's extremely hard to get it into gear once the car is moving. it seems that i almost have to drop the RPM for it to go into gear, and its somewhat intermittent. Sometimes it'll just drop right in, most of the time i had to let off the gas and shove it into gear.

I'm not quite sure these two problems are related but any advice at this point would be helpful, i'm tired of throwing money away.

i've been reading up on the net about these two symptoms and it points to a possible issue with the camshaft sensor. before my issue with the transmission my mechanic did suggest it may be a bad tensioner/belt, timing is off, or camshaft sensor, but he said to start with the plugs and coil to rule it out (and cheaper). just wondering if anyone can give some advice.

thanks!