If you did not mislead anyone about your capabilities at the interview, don't be hard on yourself.
You company hired you not because you knew the stuff at the time but because you could eventually figure it out.
And figuring it out was what you were in the process of doing until you decided to give up.
I suggest that you quit your self-talk about not being able to hack it. You can hack it, it's just going to take more time than you and the company expected. But taking much more time is probably a lot better than not getting it done. Don't compare yourself to an experienced person, because you are not. This invidious comparison is part of your self-talk, and you are doing a fine job of demoralizing yourself. Just stop it - the self-talk, the self-condemnation, the self-flagellation, the self-whatever. All the self-hectoring in the world won't get you one step closer to finishing.
If your manager is asking why you are missing milestones, be blunt about saying that the learning curve is steep and brutal - which it is, and there are tons of things that you need to figure out.
If your manager is competent, then they should ask you what resources you need. First on your agenda should be the availability of someone to answer your questions as you go up the learning curve.
Since you already missed a couple of milestones, I suggest that you be pro-active and tell your manager that you are distressed over missing the milestones and that you could use having the support of someone senior to answer your questions. Be prepared to soldier on, with or without support. They have to expect that it's going to take you more time.
If your manager asks you how much more time you expect it's going to take you, give your best estimate. Then put that estimate into context by saying that with support, you'll be much more confident that your estimate is conservative. And your ability to beat your estimate is contingent on the level of expert support you receive.
The objective reason why you are missing the deadlines is the steepness and brutality of the learning curve, which the availability of expert support will go a long way to mitigate. Stay objective i.e. professional in describing your challenges.
Stay away from the subjective editorializing, which has nothing to do with helping you resolve your situation, adds nothing to your credibility as a competent professional - you HAVE to believe that you are a competent professional. because if you don't, why should your boss? - and is quite unfair to yourself. You need to like yourself enough to be fair to yourself.
No matter how much you kick yourself for being inefficient, bear in mind that you are the best person available for this project. You may not be the best person for the project but you are the best available person for the project. What they see is what they get. Focus on soldiering on, because that's the only way that this project is going to get done.
If it's any consolation to you, you'll be a lot more effective and efficient on the next go-round. I am confident of that, and so must you. In the meantime, bite the bullet and get on with this difficult business.