For NOTES to show verify you have this option enabled, (snapshot below). First print a quote, then in Options section all the way at the bottom verify you have it checked. If you make a change in options click the REFRESH button at the bottom to make it effective.
For the other issue you reported all items as #1 did you use the ADD TO CART feature for this project starting from item#1? If so there is a case open for this known issue. What you can do is renumber items using the Hotkey "R" as a work arouond.