Parents with children who were slow to talk - how did/do you communicate to your child about manners & painful accidents

I have a child who will be 3 in February and still isn't communicating with verbal language. I'm not worried, his word count is just fine and all that but ALL of our parenting/teaching moments are us talking to him. There's really no confirmation that he understands what we are saying.

So the first situation is this: our son burps or farts and immediately thinks it's hilarious, which it is but of course we can't let on to that because we're adults or some bullshit. I dunno, I don't make the rules. Anyway. We tell him to say "excuse me" (which we know is in his vocab and has been for some time) but do not demand he pronounces it correctly. We just need an acknowledgement. So we tell him, he does the 2 year old thing and refuses so we begin to press. He gets embarrassed/nervous, can't produce the words and begins to cry and goes into a tantrum and what started as a minor parenting moment has exploded into something it didn't need to be.

As a result, we've switched to a method I'm not completely sold on which is having him say the word "sorry" after he burps/farts. He's able to get that word out no problem when prompted. The problem I have with it is that I don't want him to feel bad/shamed over normal bodily functions; I don't think farting is something that demands an apology. I'm nervous that this technique will make him feel shame over his body AND will devalue the word "sorry" to the point where he won't recognize the importance of using it correctly.

The second situation has only happened twice, last night most recently and it really freaked out and I need to be told if I'm overreacting.

We were both sitting on the ground and I was having him identify and say letters. We got to "H" and he couldn't say it and began to get very frustrated. He tried to get up and run away and as I reached with book in hand to stop him, the corner of the hardbound book caught him right in the ribs. It was a complete accident but it could not have felt good. I reached out with a lot of force and very quickly trying to stop a running child and caught him what I consider to be a very soft/sensitive area of a body.

Anyway, he immediately started cry and I began to comfort him but due to his slow development, I doubt very much that he understands what I'm telling him which was "that was an accident" "daddy would never hurt you on purpose" "we don't hurt or hit people." etc. I'm very concerned that he'll begin to believe that it's ok to be violent or hurt children if standard comfort and apologies make it ok. I'm even more concerned that the thinks Daddy is someone that will bring him physical pain in life.

First things first: am I looking too much into this? We're first time parents so I know that's a possibility. Secondly, any advice on how to communicate "ideas" to children who are less developed would be greatly appreciated. How would you have handled the second scenario differently?

TL;DR Our child isn't that developed and we're unsure about how we we should communicate with him in specific situations.