I was actually in favour of not using the NewGame+ file for the "All Quests" run, since with inichi's new discovery to duplicate power, magic and speed tabs, you can beat the game pretty quickly without any leveling up at all. But Solon has a good point to use the NG+ one, because this allows you to show off all the cool single- double- and tripple techs you would never see in any other run. Even if it wouldn't be necessary faster than a legit run with the duplicate glitch, it would be much more entertaining because of the much higher variety.
If using the SRAM file for NG+, I agree that it would be much better to use a legit one without cheats to get all the items and level ups in it, even if it wouldn't be provable in the end. Inichi's one is legit with a movie shown how it's done, but the downside is, it doesn't have every single double and tripple tech, and not every item. If you want a provable legit SRAM with all items and techs, you can always use the one I got at the end of my last 100% CT run before the final Lavos fight. The movie is available in the
ZSNES section for verification, and since SRAM files are universal, you can load it just fine in Snes9x as well. The only downside in that SRAM is that I didn't got Level 99 (but close to 60), but most of the stats are pretty maxed out anyway, so it wouldn't really slow down the run. Of course the NG+ SRAM I used in my first CT TASes is legit too, but unfortunately not provable.
So yeah, we have to weigh what is more important, a legit run that presents the duplicate glitch the first time ever, or a more entertaining run with the NG+ file.
I would probably favour the latter thinking about that now, but only if every tech gets used at least once despite possible speed trade-offs.