- can you modify weapons on the go just as you can repair them?
Yes, you only need to buy a mod (found in some merchant's misc section) that will fit the weapon, then press X on the weapon and apply the mod.
- is it wise to be distributing points amongst the skills when levelling up?
Distribute as you see fit. Obviously don't distribute points on skills you do not use. You can level things up evenly or pour a lot of points into one or two skills. I find Speech is always good to get up early.
- at the start, one of the specializations i chose was energy weapons.. is it going to be difficult to find these/ mods for them/ammo? it seems as though most weapons I encounter are regular guns.
As you proceed, it will be easy to find ammo and mods for energy weapons, as well as energy weapons themselves. No problem. Keep in mind you can use a workbench to turn microfusion cells into energy cells and vice versa.
- is there a way to get through the ncr correctional facility (for the sheriff quest) w/o getting into a huge firefight? if not, should i be able to better this at level 3?
You should be okay if you are not hated/vilified by the powder gangers. Alternatively you can wear a powder ganger outfit to blend in. Just be careful, the disguise won't fool everybody.
- what kind of resistance can I expect from a neutral area?
Not sure what you mean. You mean if you encounter a faction you have a neutral reputation with? There won't be any violence, but some powder gangers (escaped convicts, usually found in the wastes or around Primm for example) will attack you no matter what.