It's easiest if you do Lonesome Road and bomb both the NCR and Legion before ever going to the Lucky 38. I always do the DLCs first for just this reason. If I get a hostile reputation with both the Legion and NCR, I can then milk the opportunity to kill as many Legionaries and Profligates as I like and do companion quests/side quests before going to the Strip. It's also during this point that I usually visit both Dry Wells and The Long 15. You can wait to get the pardon until after you've gotten your grenade rifles.
And this is coming from someone who's never played an explosives-based character. To me, explosives are either a tertiary weapon (i.e., mining the entrance to Ulysses' Temple before the final battle) or excess weapons to sell. After returning to the Mojave, I just sell whatever mines, grenade rifles, grenades, etc. I have. I've only used grenade rifles a handful of times to see what the different types of grenades did. Same with grenade launchers and a mini-nuke launcher. For me, it always comes back to sniping in some form, starting with the varmint rifle that Sunny Smiles gives you and ending with the almighty Holorifle (I'm biased toward energy weapons).
If you want to do NCR quests between nuking both factions and going to the Strip, that's what disguises are for. Same goes for Legion quests such as teaching Decanus Severus how to disarm mines. It also makes for stealth kills if you want to play an assassin/spy character. Your enemy won't suspect one of their (apparently) own. You'd be playing less like a Hollywood ninja and more like a real ninja. After you've visited the Lucky 38 for the first time, the pardon script will trigger, boosting your reputation. In my experience, I went from Vilified rep with the NCR after bombing them and the Legion to Merciful Thug upon freeing the NCR hostages at Boulder City. Then I went from that to Soft-Hearted Devil by doing some more NCR quests with my handy disguise, and from that to Liked after speaking with Mr. House. Meanwhile, my Legion rep went from Vilified at the end of Lonesome Road to Neutral upon killing Benny, recovering the Platinum Chip, leaving The Tops, and getting the Mark of Caesar from Vulpes (or Alerio, if I killed Vulpes in Nipton).
