Bought a used 2008 6.4 and was told it had the egr deleted. New to 6.4 ranks so will be asking questions that may seem dumb to some but have to learn somehow. Old 7.3 owner so not new to psd’s. Also was told that the truck was programmed but no info other than that. Does display the service engine symbol. Also shows battery issue light but I think the previous owner put in smaller alternator. Maintains battery charges. Issue is this. Truck ran great getting 12.2 mpg pulling race trailer but when I stopped for fuel and restarted it the service engine light went off and it had no power. Turned it off and restarted it and the power came back but the service engine light stayed off. The truck does blow black when accelerating until the light went off and then it did not but after restarting it again blows black . After sitting for several hours and restarting to leave the service engine symbol reappeared and the truck ran great. Got home sat 2 days and when restarted now the indicator lsymbol is off again. Exactly what do I need to do to get this truck back to reliable as I need to take a long road trip to pick up race car. Also is there a programmer I can buy that will work with and solve my issues.

 

The 6.4 PSD is many things (fast, powerful, smooth, refined, quite, etc.) but reliable just really isn't in its nature. If you need reliable, cut your losses now and either get a different truck or swap a different engine in it.
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So two questions here. Why the black smoke and the SES light, and then what to do to minimize potential future failures.

SES light. Your description indicates that the DPF was probably removed given the black smoke.
1, Pull the codes. There should be codes stored in the PCM. This will at least point you at an engine system... EGR, CAT, DPF, Fuel. The CAT will be a problem if they did not remove it.
2, Verify hardware removed or left on. This is going to play into the second question I think.
Generally a properly deleted and coded truck will throw no codes for any of the EPA systems. This leads me to believe the problem lies elsewhere... like injectors or something else. That's it for the light. Just normal diagnostics at this point.

Reliability. The proverbial loaded gun. My opinions are my own, but I will share them here. Some things below depend on miles. A truck with 250k will probably never have a plugged oil cooler as an example. If the truck is fully deleted and none of the old hardware is available, the following list will be problematic at best.
1. Add a bypass coolant filter to help reduce the possibility of a plugged oil cooler... mileage dependent. I used the existing EGR cooler pipes. If yours are gone and plugged, that's that.
2. support the EGR exhaust pipe at the back of the engine. That pipe will break eventually if not supported and is a real fire hazard. The original horizontal EGR cooler would ideally be left in place.
3. Leave the original EGR valve in place if available as it might act as a runaway preventer. The butterfly does close for a time with ignition off (the jury is still out on this)
4. Drain the water separator regularly. Water will kill the injectors faster than a .44 Magnum.
5. This engine has top-end lube issues at idle. Don't idle for excessive periods if avoidable. Depending on mileage, preventively replacing the rockers is a possibility. About $1k last time I checked for a proper job.
6. Add an oil catch can or vent to atmosphere for the PCV. My opinion is I see no need on a deleted truck to send a potential fuel source directly into the air intake.
7. There are a lot of posts about the "Best" tuner so I won't weigh in here. I will say that I never intend to run my 6.4 on anything other than the "Stock" tune. I see no reason to invite disaster.

The single best advice I have read on this site is:
Drive it like an adult: Maintain it like a madman; Save your pennies for the inevitable failure. I wish I remembered the source of this great advice.
Diesels are not cheap to maintain, and this engine with its limited production volumes is even more so.

I hope my opinions did not bore or annoy you and Good Luck.