There's no sealant, just a gasket. If the glass was replaced before, the gasket may be out of place. If you aren't concerned about aesthetics I'd just run a bead of sealant around the gasket. Your glass guy likely has a better solution.
A Nexiq USB-Link 2 is the recommended interface tool. This also works with a wide array of different diagnosis programs, like Isuzu IDSS, Allison DOC, Cummins Insite, Wabco, and probably many others that I don't have any experience with.
Deletes are so hit and miss. It's really hard to say.
If you unplug the EGR , does it set EGR codes?
If I'm not mistaken, there's a short section of harness between the VNT and the main harness. Make sure both ends are securely attached.
Cvip?
Relay clicking is normal.
You're gonna need to get the codes from the ABS module. A generic HD code reader should be able to pull these codes from the round 9-pin connector.
I know you went through the fuel tank and everything, but also check the inlet fitting on the fuel filter too. Previous debris from the fuel tank gets caught in the banjo bolt. If there's another adapter fitting between the banjo and the filter housing, pull that too and look inside.
Pieces may be in the rail. I'd take em all out, take the rail off, wrap it in a clean rag, then blast with compressed air and see if anything comes out.
The steel tanks on these trucks are a constant source of rust chunks and other junk. I don't know how this got past the fuel filter. I don't think this enough to seriously restrict fuel flow. If it was it'd set P0087, P0088, or possibly both.
I'd remove the flow dampers and fuel supply line...
The firewall one. It looks pretty good in there.
Does disconnecting the scv make a difference in how it runs? In theory it should still run when disconnected, just badly. The best way to tell if it's bad is to watch it's performance using DX.
P0193 in Isuzu literature describes it as a large...
Get it started and start wiggling connectors. A bad connection at the common rail pressure sensor can cause some misfire symptoms. Scv too.
I don't like telling people to buy thousands of dollars of parts on a guess.
Uo101 doesn't mean anything if it's inactive.
P0102 and P0113 were set when you unplugged the MAF sensor.
P0183 is the fuel temp sensor on the fuel pump. The sensor pretty much never goes bad, so I'd suspect wiring. This will cause limp mode.
P0193 is the common rail fuel pressure sensor high...
A scan tool with live data may be essential for fixing this. I'll continue to think about it.
Had anything been done to the truck before the problem first started?