@DHERO
First I would recommend trying to replicate the same caution that you have in SF in MK. In SF if you mind is blank and you dont know what to do, you never stand in idle, you hold down back, in MK, hold down and block. If you need to walk forward, let go of block, walk, then go back to down block. What will feel different is letting go of block to walk back and being vulnerable, whereas in SF you're automatically protected with auto block (as long as its not a low).
I totally get the "sitting duck" feeling you described. I'm an MK 'convert' myself. I played the hell out of SF4 then switched over to MK9 and what helped me was to play matches vs the AI on hard or hardest with only the block button and tried to run out the clock. It's not the most fun thing and its a little wack, but try it a few times. If you run out the clock, you win. What you will find is that since you're isolating block, thats the only thing your mind has to work on, so you will improve quickly. I did this in SF too when I started to learn and it helped immensely in both.
To your questions:
1. Most of the time you will be holding block, but if you try to Flawless Block after a gap in a string, you will be tapping and releasing block to do the u2/u3 punish. It kinda feels like an option select. Note that you cannot do an u2 or u3 after a Flawless Block if you are still holding the block button.
Go to this link and pick out a string with a gap and record it in training mode. You will hold block until the gap, release block, and press it again about a frame or 2 before the next hit in the string connects.
https://testyourmight.com/threads/list-of-all-gaps-in-characters-kombo-strings.69441/
2. If you are at frame disadvantage, you should be blocking 90% of the time, since there are no invincible special moves or moves that have instant armor. Keep in mind as you wake up, the u3 is fully invincible, but you have to be knocked down first, and the Fatal Blow's armor starts around frame 5 or so.
3. d1 and d3 are like mini hit-confirms. If they are doing it to you, block it and they are always at disadvantage so now its your turn. If you do one and it gets blocked you should block, if it hits, then its now your turn with double digit frame advantage. There are no links so nothing will combo no matter how high your advantage is, but now you can do a standing low attack (usually b3) or maybe even an overhead if you have enough advantage so there's no gap for them to counter poke you. Btw, if you go for a down poke, always hold block right after you press the button, if they block it, you dont have to do anything else, youre already blocking (kinda like holding down/back whenever you do a crouching attack in SF), if your poke hits, let go of block and take advantage of their frame disadvantage. I hope some of this helps.