Hmm yeah it can be tough to know where to go...what kind of character are you playing? What are your special stats? 

The thing is, most people spread there points too thin when they first play. Keep your perks tight and boost damage given and damage incoming as priorities. 

Take a look at Lone Wanderer - big boosts to both if you like going solo. Also - check out the AGI multipliers for sneak damage which can help a lot if you're not going for a tank type of build. 

Specifically for the armor - if you're still at the level where it's only leather, metal and raider...just go with some leather and upgrade it as much as you can. Even better, dont' forget to check with vendors. Myrna has a "Wastelander" chest piece in diamond city for about 1000 caps way earlier than you could build one for that protection. Lucas miller has a nice metal "Champion" arm for about 800. Caps aren't hard to come by either. Just loot ammo, chems and make new chems and resell. (amongst other tactics).

Hope that helps...

Cool - so personally I would reccomend picking one of gunslinger or rifleman at the beginning. Trying to be a jack of all trades isn't the best way to go in the Wasteland. Like don't perk both of those. Just figure out which weapon feels better to you (pistols or rifles) and perk one. Then I owuld prioritize lone wanderer and sneak to trigger sneak multipliers. Even if you're not going to play a stealth character, it pays to be able to get closer to enemies wihtout them hearing you.

Those two perks will really save you a lot of headaches.

Also, stop perking gun nut. You'll end up looting better weapons. 

Take a look at this for more ideas on your character: http://www.levelbased.com/guides/fallout-4/tools/special

That's the idea - yes. Specialize early on. You can always add perks later. You'll find you have more points than you need once you get the hang of it. 

And yes for modding. Just take stuff you've looted to your home base and strip off any mod you want from it. Or, find a vendor that's selling what you want. (Like farming for an enchantment in Skyrim). 

The problem with adding points into gun nut especially is it becomes redundant. You'll have enemies drop sick weapons all modded out. Or at the very least pieces of what you're looking for. For example, you find a base combat rifle with a .45 reciever, no goodies. But you can go to Arturo and find one with a Marksman's stock. Then a raider will drop one with a long barrel. And at some point you'll have so many caps, you can just go buy Overseer's Guardian with a .308 mod. 

For example :)

Yeah if you are itching for spomething specific - you can def go that route. (SPOILER) But, tbh if you join a certain faction, you'll get the best silenced 10mm pistol in the game for free :)

I guess it depends on how much you want to know, and how much you want to find out. I don't want to spoil stuff for you...