To answer your question #1, your best option is MRT Stage 2 tunes and EOC delete parts, all via EOC. If you cannot do it yourself, find a local shop to do it. It's not hard, just labor intensive.
Here's how
Pull out the starter relay (in the fuse box).
Put the key in the RUN position.
Take a short piece of wire and jump between where pins 30 and 87
of the relay would go. if the relay is labeled 1-2-3-5, jump between
pins 3 & 5.
I have no experience with Tuner Depot but can say if you want to turn off the EGR the GDE compliant tune does not do that. I'm running the MRT, via EOC, stage 1 tune that shuts off the EGR. It has a handheld device that allows you to select their 20hp or 40hp tune or change back to the OEM tune...
They will only answer emails and demand you only send one as multiple emails seem to antagonize them.
Regardless of their customer skills, they can be trusted
I was told by a Califunny smog equipment inspector that sniffing a diesel with the gas sniffer will ruin the sniffer. And a diesel sniffer has been developed, he didn't know why. Even if they could sniff a diesel they still have the requirement to check for non CARB approved aftermarket parts...