The post is general so my response will be in general.
If you haven't monitored the truck, this should be done ASAP. If you don't know what parameters (PIDs) or how to monitor, check out the stickies in the forums. Your truck needs to be in GOOD health. Tunes will expose and exploit any weakness (injectors, warped heads, ect). I'm not sure what "level 3" tunes are, but I can assume you are talking about higher horsepower tunes reserved for trucks with head studs. So, it would make sense to install head studs and have your cylinder heads inspected by a reputable shop familiar with 6.0L powerstrokes. Factory heads have a reputation for being warped (mine were 0.009") so having a flat gasket surface along with head studs will be the best insurance for a solid motor. (My truck had H-11 studs but no head work and I blew a gasket which is why I stress machining the heads, too)
With flat heads, studs, and an egr delete your engine has a solid foundation for power and reliability. Monitoring the trucks vitals is important, too. With higher power tunes I highly recommend a pyrometer to protect yourself from heat related failure and fuel pressure gauge to protect your injectors. Most stock injector trucks can maintain proper fuel pressure with some 6.4 banjos and a blue regulator spring.