Paris pass vs pre-purchased museum tickets

will having tickets to these places pre bought and printed enable me to skip the lines the same as the museum pass?

Yep, you skip the long lines that form with people that neither have a pass or did not buy tickets in advance.

Also, I noticed that the museum pass is to be bought at the museum itself. Wouldn’t there be a long line for that, same as the museum ticket line?

Maybe but you are not limited to buying it at museums you can buy it at the airport when you arrive or FNAC book stores and tourist info centers through out the city.
http://en.parismuseumpass.com/rub-t-points-of-sale-3.htm?cat=3

We bought the museum pass at the Pantheon, which was near our hotel. Since the Pantheon is not heavily visited, there were no lines to purchase the pass.

The Museum Pass (NOT the Paris Pass) sometimes gives you access to designated security lines that are shorter than the unticketed line. A ticket or pass -- makes no difference at security. At the Louvre there is a special line for those with passes/Tickets at the Pyramid; in my experience it is faster to enter the Carrousel entrance where no ticket or pass is needed. At the Orsay, there is a separate entrance for those with tickets or passes; very much worthwhile having ticket here to avoid long lines. There is a separate security line at the Orangerie. Makes no difference at Versailles, Ste. Chapelle or Notre Dame Tower.

Eiffel Tower is not included on the Paris Museum Pass. Notre Dame is free, although the tower climb is covered by the pass (still requires a same-day time reservation.)
If the items you listed are truly ALL you want to see, pre-purchased timed tickets look like the best deal.
We have never bought tickets ahead except for Eiffel Tower. Usually get the Museum Pass at a less-busy location (Cluny, Invalides)

If you are looking at going up the Notre Dame Towers you will need to reserve your time the day off. There is a machine located on the left side, facing Notre Dame, where you would line up to enter the Tower entrance. Begining at 7:30 am the day of you could print out your time or use their App. and select your time from that. About 10 minutes before your scheduled time, get in line. You will not need to show your Museum Pass or purchase the ticket itself until you head part way up the stairs to the Gift Shop / Reception Room. Here is where they check the Paris Musuem Pass or purchase your visit for the time. The App is now called DuckTheLine.

ND Info: http://www.tours-notre-dame-de-paris.fr/en/News/No-more-queuing-to-go-up-Notre-Dame

If you haven't already done so, check out the pre-visit information on the Catacombs website. There are references to potentially long waits in line. They do offer a "quick access" ticket to speed things up. It's 29 euros for each adult.