Great, you're nearly there! Well done! It's really a steep learning curve at the start, much of it is finding a technique which works for you and the process which you find 'makes sense'. The limit screws are best avoided - at least until changing cassette or wheel, but it's too late for that now (why I said about setting them without the cable involved - that's just my way of setting them once & then mostly forgetting they're there). The barrel adjuster is your indexing for those couple of skipping gears - viewing from the rear you should be able to tell which 'side' the chain is rubbing on the cassette making the noise (you'll see it rub, or even 'jump' to try and change, then fall back). With indexing you're basically moving the derailleur arm miniscule amounts to stop that rubbing (use quarter turns!)... But also not too much that when it is time to move, it moves the right amount for the chain to change cogs. Quite a lot of the time you may end up 'pushing the problem' to other gears... At this point that's fine - try and push the problem to the end of the cassette you use less (higher gears?).
If your hanger is slightly bent (more than likely) you'll never be able to get indexing 'perfect'.
If your chain/cassette/chainrings are worn it'll never be 'perfect'.
If you've messed with limit screws unlikely it'll be 'perfect'.
If your front derailleur angle has changed/been knocked it will not be 'perfect'.
So what I'm basically saying, at this point don't chase perfection! That can come in time as you gain the skills and tecnique - along with new parts and any time your bike goes into a workshop for something, always see if they can 'spare 5 mins' to check the indexing while you're there so you can see how they do it (with you there it will be a quick check and likely they won't even charge time for it).
I found usually making my 'easiest' gears in my lower chainring rub a little was ok, or my absolute highest gears in big chainring. I used them infrequently enough that having noise when I did - for easier indexing and good gears for the rest of the time, I was happy. As I upgraded and got better with maintenance it got better and better, easier and easier to index.
Sure it's a Giant Defy 1 2014 with the Sora setup? Probably a Defy 2 or 3 - the Defy 1 would have come with 2x10 drivechain as was 105 level (with probably Tektro brakes and non-series shimano R565 cranks). My
2015 Defy 1 came with the same brakes (and the FSA gossamer cranks they used) with the switch from 10 to 11 speed 105. Pretty superfluous at this point - the Deore 9 speed chain will work with any of Shimanos 9 speed groupsets (that era Sora, Deore and Tiagra overlap a lot).
Your shifters look like the Tiagra 4501 with the side entry cable -
https://www.sjscycles.co.uk/gear-shifters/shimano-tiagra-st4501-9-speed-double-road-sti-levers/ ? Which probably means your Rear Derailleur is the 4500?