First time building professional website

Man oh man.

I have a somewhat decent understanding of HTML and CSS with little experience in Javascript. No knowledge of PHP but think it's going to be required moving forward with this project.

Basically where I got hired, I'm the graphics and marketing specialist. I run the social media and website as well as any graphic requests like flyers, banners, etc.

I have a lot of experience designing website and some building, but nothing on this scale. Building my company's website from scratch.

It's currently made from a CMS called 'Craft' and it just sucks. It's like someone builds you your own personal WordPress. It is SO limiting and we are wanting to move away from it to something we have total control over.

There's no time limit on this and not in any rush to push it out, but this is what I want to transition into so I'd like to move forward with it ASAP.

It's a nonprofit, mainly informative website that I'd like to be responsive. The HTML is the easy part, CSS is where it's starting to get tricky and I want to make sure in writing clean code.

Where are the hest resources to learn everything I need? I'm using Lynda.com to brush up on everything like Bootstrap and Flexbox.

What are some tips moving forward that could save me tons if headaches?

Any and all advise is appreciated. Thank you so much!

Edit: Just for clarity sake, I would classify myself as a front-end developer. I don't know any backend languages yet and will be learning them as I go.

They're not trying to get the greatest website ever created. Just something that looks and acts good that we have full control over.