There are plenty of tools online, both free and paid, to combine pdfs into 1 file. One free one is ilovepdf.com
You want to give them as much info as possible so they dont have to request additional documents. I for example created a 27 page pdf to proof my business. I spend 3 days on it too.
Nothing will happen. If you just leave the country then no problem, no one will ever check and there won't be a fine when leaving.
The problem only exists if you want to extend your visa at an immigration office in the country. Then they check and you pay 1900 baht fine if you did not do the report. I actually know several people on long term visa that never do the 90 day report and just pay the fine once a year.
The application only asked me for a flight number so I just went on skyscanner, selected a flight and entered that flight number. I did not buy the ticket yet but I will if they ask for proof. I am currently waiting for approval.