For physicals, you want to be using Elemental to 2x the damage they deal; a lot of the Materia had elements added (Holy to Restore/Revive, for instance) to take better advantage of that. Back row should be avoided if the character doesn't have a ranged weapon (and Barret has a case for front row even if using a gun as his innate changes to a strength boost).
In the Bottomswell fight, assuming it was the normal mode one, it's the ideal time to try out the first Summon Choco/Mog as the boss is weak to wind. It can either be used early to skip ahead from the initial phases (tail attacks, etc.) or later on when Waterpolo bubbles are getting sent out as it'll hit both the boss and the bubble.
This boss can also be poisoned; if you have a handle on things defensively, then you can cast Haste on the boss to accelerate the poison damage (whereas Slow decreases it as the ticks proc less frequently).
I think in your set-up that Aeris would have been a better shoe-in for the Bolt Materia as her Magic stat will typically be higher at this point (depends on the rank-up options that were picked, if one was available when it was unlocked). It'd be a good idea to pick up a 2nd Bolt Materia somewhere as there are a lot of mechanical bosses in this game and having it for Elemental/casting is always handy.
I finished the 2.0 versions of these fight recently; I could have a go at scripting Godo to use his 3 forms in sequence with different properties to each, and beating them advances the fight or something to keep it with the theme of the rest of the Pagoda.
Yeah that's right; it's all variables and IDs which stay the same between versions. When I scripted NT I mostly left the vanilla variables alone so there's not much interference between the two.
Not sure what the cause there is; some Accessories and Armour have an effect that prevents the application of Barrier/MBarrier (Amulet accessory, for instance, prevents all barrier-type magic. Ribbon also blocks it). Might be that.
It's in the same place as it always is, the sewers: