I JUST found an available machine that I could pull the toolkit log and you're correct about the 5000 being deferral code... I should have waited a bit longer for a machine to become available ;)
[30-04-2014 15:07:14] [Pre-Installation] Setting deferral history...[DeferTimesRemaining = 0]
[30-04-2014 15:07:14] [Pre-Installation] Creating Registry key [Registry::\HKEY_LOCAL_MACHINE\SOFTWARE\PSAppDeployToolkit\DeferHistory\Adobe_Flash_13,0,0,206_EN_01]...
[30-04-2014 15:07:14] [Pre-Installation] Setting registry key [Registry::\HKEY_LOCAL_MACHINE\SOFTWARE\PSAppDeployToolkit\DeferHistory\Adobe_Flash_13,0,0,206_EN_01] [DeferTimesRemaining = 0]...
[30-04-2014 15:07:14] [Pre-Installation] Adobe_Flash_13,0,0,206_EN_01 Installation completed with exit code [5000].
As for the -1, I believe I will have to use that method of dual deployments... something I try to stay away from since it can cause some clutter and confusion. It IS showing that the -1 errors are slowly decreasing, which I would assume is due to a user eventually logging into that machine for the install to go through.