Interesting battle. I call stalemate.
Naraku does have the upper hand, but Father is up there when it comes to hax'd.
Honestly could see this battle go either way and is gonna be ridiculously long with the means both characters have to sustain themselves (Father with the millions of souls in his body, Naraku with the countless demons fused to his body). Naraku has the advantage in destructive scope and durability, but Father's abilities granted to him via Truth should grant him an expanded scope of abilities than what Naraku can muster.
@AFGM: What the panel shows is Father forming nuclear fusion within his hand, his words ("I wanted to avoid destroying this place, but I can always reconstruct it afterwards) implying that the release of the energy would be comparable to a hydrogen bomb.
I know Naraku has tanked attacks waaaay more powerful than those displayed on FMA, but i think Father's shield is atleast on par with it.
And he showed a ridiculous mountainbuster blast at the end of ch 106 that i can't upload right now...
The thing is they are "in character", so i could picture Naraku using his cunning ways to drag the battle enough for Father to lose control over "God"...
Still i'd give it to Father 6/10