I essentially want to play a 'smarter' character who has a bit of understanding of guns and flame-throwers. He's more intellectual, and i'd rather not have to start cranking points into Energy Weapons (since I hate them) just to get a decent use out of a flame-thrower.

So I am wondering if there are any mods that rework the gun energy weapons skill to move any 'flamer fuel' based weapons to the guns skill.

Thanks in advance for any help.

Can't you do it yourself?
Just edit the base weapons and unique weapons to be governed by Guns and edit the perks for fire weapons to require Guns instead of EW/Explosives.

But why though?
If you want to specialize in two weapon groups then you should be forced to spend points on both of them.
Moving Flamers over to Guns would be cheating the game desing IMO.
Action and consequence, your choices have downsides to them, you want Guns and use flamebased weapons? Then you should be forced to put points into two skills.
That's just my opinion, but choices should have consequences to them, if you're gonna cheat the game desing like that then what's the point to playing an RPG where choices and consquences have been designed to matter?

Anyway, go to GECK, to to the weapons tab, find Incinerator (Heavy and standard), Flamer and Flare Gun then open them up and change the skill it belongs to.
Simple as that.
Next go to Actor Data and Perks, find the flamer based perks, double click them and on for example Pyromaniac change: GetPermanentActorValue Explosives to Guns instead.

Might take a 20 minutes if you haven't used the GECK before but it's really simple.