The non continuous monitors, O2/evap/cat should eventually complete their test provided no error code.
The misfire monitor all four cylinders pass so assume no misfire error code pending/set.

When the misfire error code sets post the freeze frame data that gives RPM/engine load/ECT etc.
Post fuel trims LT/ST and MAF g/s from idle up to 80% engine load.
Also post the A/F sensor voltage at 80% load.
Trying to determine under what conditions misfire codes setting.

Can you reproduce the misfire by wiggling/tapping the coil or injector connector/wiring?
If can't be reproduced then may be time swap injectors.

 

I wiggled the wires with no effect. I swapped the injectors and it still set the same code. Here is the freeze data.

Vehicle VIN: 4T4BE46K89RXXXXXX
Vehicle Manufacturer: Unknown
Vehicle Calibration ID: 333A5300

Freeze frame information:
------------------
Fuel Status = 0 byte
Engine Load = 45.882 %
Engine Coolant Temperature = 60.8 °F
Fuel Trim Bank 1 Short Term = -7.031 %
Fuel Trim Bank 1 Long Term = 5.469 %
Engine RPM = 1,372.5 rpm
Speed (OBD) = 0 mph
Timing Advance = 14 °
Intake Air Temperature = 42.8 °F
Mass Air Flow Rate = 8.12 g/s
Throttle Position(Manifold) = 20.392 %
Run time since engine start = 43 s
O2 Sensor1 Equivalence Ratio = 0.99
Distance travelled since codes cleared = 1.243 miles
Barometric pressure (from vehicle) = 14.069 psi
O2 Sensor1 Equivalence Ratio(alternate) = 0.99
Catalyst Temperature (Bank 1,Sensor 1) = 602.6 °F
Catalyst Temperature (Bank 1,Sensor 2) = 62.96 °F
Voltage (Control Module) = 14.042 V
Engine Load(Absolute) = 24.706 %
Commanded Equivalence Ratio(lambda) = 0.995
Relative Throttle Position = 1.176 %
Absolute Throttle Position B = 53.333 %
Accelerator PedalPosition D = 15.686 %
Accelerator PedalPosition E = 31.765 %


End of report.

The engine coolant temperature and Catalyst Temperature (Bank 1,Sensor 2) do not change with the engine just started or when it is up to running temperature. The real time info on my scanner show the correct readings. Also the engine temperature gauge shows the correct temperature.

 

Seems like everything has been covered except the cylinder compression.
The freeze frame data looks normal.
Misfire happening at start up/engine could be intake gasket leaks or head gasket leak.
Probably time for compression leak down test to see if cylinder losing compression .
Don't know if your set up to do the test.
Shop an easily do this for you.

 

The coolant temp stays at 60.8F. It does not change when the engine warms up and I do another freeze frame. The car temperature gauge and my scanners realtime scans show the temperature going up to 190 degrees.. Is that normal?

Also the "Catalyst Temperature (Bank 1,Sensor 2) = 62.96 °F". Should that temp be 500 degrees below the Bank 1 Sensor 1?

 

"The car temperature gauge and my scanners real time scans show the temperature going up to 190 degrees.. Is that normal?"
This is normal.

"The coolant temp stays at 60.8F. It does not change when the engine warms up and I do another freeze frame"
Freeze frame is a snap shot of the data(auto set by the PCM) at the time the error code was set.
So if error code was set when coolant temp was 60.8 F that is normal.
Can't say why you are reading 60 degrees freeze frame ECT when the engine is at operating temp.
Don't think it's related to the 2 cylinder misfire.

 

"lso the "Catalyst Temperature (Bank 1,Sensor 2) = 62.96 °F". Should that temp be 500 degrees below the Bank 1 Sensor 1?"
Believe the cat temp output should be around 100 degrees hotter than the input at full operating temp.
If engine temp is cold, as read on your scanner, the output cat temp would be cold and increase up to maybe 700 when engine is at operating temp.
You can verify by monitoring engine temp vs cat temp.

 

I think I found the problem. I noticed the coolant tank was a little lower than it was. I took the radiator cap off while running. I am getting bubbles of air in coolant. I did a compression test and when testing #2 & #3 the coolant rose in the radiator. Testing cylinder #1 #4 did not raise the coolant in the radiator.
#1 190 psi
#2 170 psi
#3 165 psi
#4 190 psi

I think the head must come off to check the head gasket. The new spark plugs (except #4) have an ash build up on them with less than 50 miles on them.

What is a good service manual. I don't want to spend a lot since I may never use it again.

 

I use AllData but have never replaced head gasket so will defer to other members.

Just to confirm your finding the auto stores will loan chemical tester for combustion gas in the coolant.