Sile2001

No, you put "Yes". You don't have to file 2018 taxes until April 15.
 
Yes. 
 
Yes. 
 
No. They may request 2018 tax returns later, or at the interview. Not in "problem" way, but in a "we'd like to make sure nothing changed" way. 
 
No. It's perfectly acceptable to file in April and it's not yet April. Very normal. 
Perfectly acceptable to show 2017 taxes, most people would use 2017 taxes since most (all?) people don't have 2018 transcripts yet. You couldn't even file taxes for 2018 until a couple of days ago. 
 
No, just pay the taxes owed in a manner acceptable to IRS. 
As long as everything is in order and IRS has a plan, you're fine. 

The PDF says that, but I just walked in with my wife like I belonged there, showing my US passport on the way in, and nobody said anything. I didn't ask permission or look unsure if I should be there, so I got to wait in the waiting area with her (about 3.5 hours total). Just keep in mind that the official rule is that you can't go in, so don't make a fuss if they choose to enforce it. That doesn't help your wife.
 
Good thing I went too, since the lady accepting the documents gave my wife pushback on the AoS forms not being uploaded to CEAC (even though I had an emailed the embassy explaining that CEAC didn't even give me the option to do it, and I had a copy of their reply saying to just bring the docs), and also was demanding my W2 even though their own website says that in our situation, a tax transcript supersedes any W2. Sometimes they don't know their own rules, and I had to politely but firmly educate them.
 
Of note, we had the same misconception that you do. The Tokyo embassy doesn't really use "rooms" for the interview, it's a lot more like the teller windows at a bank counter. You can go up to the counter with her, but I recommend standing back behind her, as it is very important for her to be the one to be handling the interview. Only answer a question if she is unsure and asks you to help. Do *not* be jumping in to answer questions for her, as that will be a red flag to the immigration officer. If you have the type of personality that always interjects into conversations or answers questions that were asked of other people or likes to control a situation (not criticizing, just saying to be honest about it), then do your wife a favor and let her go up to the interview window alone.

If you have no intention of immigrating, why don't you just call up USCIS customer service, explain the situation, and ask them to have an agent/officer send you an official letter containing instructions as to how to proceed? Nothing says "I did it your way" like a sheet of paper with the USCIS logo on it...