I don't understand what is 全能な少女の駆る聖杯戦争 means in this phrase.
I'm not sure if "almighty" modifies 少女
Yes, 全能な modifies 少女.
I'd say only 聖杯 in 聖杯戦争,
It says what kind of war (or competition) it is, thought what exactly 聖杯 means varies depending on the context.
聖杯 generally can be translated as Holy Grail but I do not know it if fits in the context.
however I've never seen something like this before, so 少女 I guess?
Please see the above.
Also what is 駆る means in 少女の駆る聖杯戦争, I've seen examples like ジェレミーの駆る日産GT-R, however the meaning seems different from this one.
駆る (karu) means to drive a vehicle or drive someone/something (in the sense one urge or force a horse forward, for instance).
What does 駆る here means is, again, up to the context.