Keep in mind, I’m still learning. I still struggle with this as well. However, I do have a tip that has helped me a lot when I run into sentences that I don’t fully understand despite knowing all the grammar/vocab in the sentence. I’ll just take one of the sentences you highlighted and show how I would go about deciphering this.
祖父は、いつか自分の船がもてたら長室におくんだといって、一つのランプをたいせつにしていた
Step 1: Remove what doesn’t make sense.
Since all sentences in Japanese MUST have a subject and a verb, it’s easiest to take out the foggy parts and look at the core of the sentence. In this case, since you have multiple parts that are making it confusing, it’s best to just reduce it down to its simplest form:
祖父は[something]といって、一つのランプをたいせつにしていた
I put [something] in there because the verb 言う is acting on an object, which is that whole block we took out. So this just helps clarify the new broken down sentence.
Step 2: Figure out what the new sentence says.
It should be much easier now that we’ve removed the fog. Looking at what we have, we can translate this to along the lines of “My grandfather, who cherished that lamp, said [something]”.
Okay great, now we have the general idea of what the sentence is saying. Now we just need to figure out what’s hiding in the fog.
Step 3: Break down the fog by putting it into its own core sentence.
Let’s look at いつか自分の船がもてたら first - you mention two parts in here being a bit confusing. Well let’s remove いつか自分の and simply look at 船がもてたら. We can break this down even more and just look at it without any conjugation to get 船が持つ meaning “(I) have a boat”. What’s great about this is that it can’t get any simpler. By having a basic sentence like this means it makes it less overwhelming and you can now target anything that might not make sense much easier. For example, it may not make sense why が is being used here, but by having it in such a small sentence you now have the ability to simply just focus on this one thing that is confusing and find an answer (at least, this is helpful for me).
Well cool, now we can work our way up! We can change this to 船がもてたら (持つ goes to potential + conditional) and we end up with “If (I) could/was able to have a boat”. Cool, we’ve moved this out of the fog and we can repeat this process until everything else is cleared up… and then we can put it all together.
What I think is great about this process is, even if time consuming, it utilizes what you already know to figure out what you don’t know, or to help you unveil what you DO know but couldn’t see at first because it was being written/said in a way you aren’t used to yet. And, not to mention, the more you do it the faster it becomes. I also think doing this in general helps your brain see more clearly how Japanese is working on a deeper level which, the more you do it, will likely reduce the amount of times you’ll need to use it because you’ll keep in memory what you learned from the previous time you did it. But idk, no research behind that, just going off of what I’ve somewhat have experienced.
Hopefully this can be somewhat of a lighthouse for you when there’s too much fog 
, I just really vividly remember this stage and how it made me make the link between conscious and unconscious understanding, regardless of whether or not that is even a good analogy 
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. For me, highlighting and hypersubvocalizing are new, and the breaking up of sentences, I really should be doing more… Well, let’s keep going, one day we may look back and notice we already didn’t have anymore fog for ages, and sit down to look at the sunrise
