So, I'm new to warhammer rpg as I was recently invited to come give it a try by a friend who runs a group (he basically brought me on as filler since he couldn't get enough of his other regulars from other rpgs). So after getting a lot of the books and reading my butt off to decide what to play, I end up choosing a Salamander apothecary. After asking the GM(friend who invited me) how to use some of the crafting based skills available he said he didnt know and would look into it for  the next session.

He said he was using Black Crusade rules to help fix combat, and we would be tweeking our house combat rules as we test them (he says default rules are too overpowered).

Anyway, not being able to wait, I spent the next few days doing nothing but collecting all the rules I could from the books and forums. After presenting it to him he said the crafting rules where still to vague AND that he was just going to cut crafting entirely.

Reason: He said that acording to the lore, space marines don't get to keep anything, ever, because they don't know how to build anything anymore. And thats why a space marine suit is worth more than the marine. So crafting AND craftmanship rules got amputated entirely based on that.

EDIT: Although, I have a feeling hes only saying that, because he said "This is why I don't like playing with you ___, you always try and do complicated #$%*."

And I respect the fact that hes the GM and hes running the game "his way", I still feel hes just being lazy and using lore as an excuse (but I'm new, so I'm not 100% sure).

So, what I'm wondering is, if there is actually Lore that supports the given rules that allow crafting/craftmanship/item ownership? And, if there is a more comprehensive crafting guide/rulebook/rule-amalgamation?

I'm currently running a Salamander who can't even use his solo mode ability (let alone craft/use Artificer) because I'm not suppoesd to be able to own/craft anything. It's heresy!~

He's partially right, now one knows the mechanics of building things anymore. They still do, just following sacred blueprints and working by rote, with little to no innovation. The salamanders, like most Astartes have a basic knowledge of the rituals of repair and construction. The Salamanders in particular are good with working with metal, and generall their gear has a even higher build quality than normal. 

I don't think Deathwatch actaully has any crafting rules built in, though I suppose you could take the rules from Black Crusade for that, It just wouldn't be a big part of the game, DW isn't really about building weapons, as it is about using them. You should have access to Artificer, and your friend is largely wrong about technology in 40k, which is fine as there are so many misconceptions there. 

The fluff also contradicts itself very often.

Space Marines do get to own things. Right there in the Armoury. They're called Chapter Trappings. Also there's Signature Wargear.

A Techmarine, after advancing into Forge Master, can craft Astartes gear with the right equipment and resources at hand, and the Trade(Forge-Master) skill.

In fact, any marine can make something with the appropriate Trade skill. My character is the team's Remembrancer, and he makes trinkets to commemorate the kill-team's victories.

For weapons, the crafting rules can be found on 147 of the core rulebook. To craft Exceptional- and Master-Craftsmanship gear, it would probably take a number of extended tests on the relevant Trade skill. If Armour is Master-Crafted, it's likely to be Artificer Armour, anyways, so just go with that.