Are there any games with models or board games even that focus on guerrilla warfare? This could be modern afghanistan, vietnam or even very old wars that involved a 'lower peasant fighting force' against a then 'modern army?'

I find it difficult to adapt LOTR or FoW or 40k rules to this as it is all about conventional fighting. Any suggestions on how to make up a game would be awesome!

I'm no expert in gaming but I'm sure that a warband of wood elves with bows and elven cloaks will do just that. Hit and run

Plenty. I'd suggest asking on The Miniatures Page.

Force on Force
Skirmish Sangin
Flying Lead: Hearts and Minds
FNG
Buckle for your dust
Charlie don't surf
The men of company B

These names spring to mind, but there are a plethora of Vietnam rulesets in particular.

It's about victory conditions, scenarios, and some special rules for flavour. In LotR, The Scourging of the Shire rulebook is excellent for hobbit guerillas against totalitarian thugs!

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I agree with lord of the nine, wood elves, woses, morgul stalkers, and hobbits can all be fielded as Guerilla armies if you are playing with enough terrain.

I think you are not really understanding this type of conflict. Guerrilla warfare is over a prolonged period and its more about the psychological toil than anything else. By the rules in the rulebook you are just focused on a single battle rather than a war.
With the rules you could fight battles in this way, providing you select your troops appropriately, but again it would have to be in a multi-scenario type game. Where one battle impacted the next

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Thanks for the suggestions, will definetly check out all those games.