2008 5.4 Roush F150 Supercharged Tune VVT Disabled

Hello, I am new to this so please bear with me. I have done a lot of research, and wanted to ask these questions after getting a general idea of how this all works. I have a 2008 F150 Roush that I acquired with a blown engine. I installed a new engine and I'm trying to get this to where I can legally pass emissions.

Here is the current setup:
Rebuilt 5.4 with Cam Phaser Lockout
PCM currently has VVT Disabled
Shorty Headers with stock cats and 02 sensors

The reason for my post is that I can't get the EVAP and o2 cycles to complete, even after driving this for about 2 months straight. When I ran the VCM Scanner, it shows that following are not enabled. Is there a way that I can enable these in order to complete the drive cycle?

Monitor Status: Evaporative System (SAE) Not Enabled/Complete
Monitor Status: Oxygen Sensor Heater (SAE) Not Enabled/Complete
Monitor Status: Oxygen Sensor (SAE) Not Enabled/Complete
Monitor Status: Heated Catalyst (SAE) Not Enabled

If there are any files or logs that I can upload to make this easier to translate, please let me know. Thanks in advance I appreciate any input.

You gotta have the fueling, MAF, & headers properly accounted for in the calibration if you want to post up your stock read from the Roush I can help. I have a lot of experience with the Roush trucks and should be able to get you truck to pass. Mine is on E85, long tubes, Cats, evap, a saleen series 6, a return fuel system etc and see always passes.