Tuplet formatting a mess

I am trying to create a cleaned up version of a song I downloaded. Its formatting was randomly spaced and messy.

Anyway, my thought was to create a new score, reset Style to default in the downloaded score, and copy from measure to measure into the new score. Trying to do at least 5-10 measures at a time and watch for problems. Boy did I find problems (see attached).
Note that I tried to make all elements visible (not just selecting Show Invisible). Also most of the tuplet brackets were set to none, I set a couple to Bracket, and noticed the brackets were rather far away from the number.

Assuming you see what I see; The tuplet 3s in the first four measures are scattered all over. I have repositioned a few which fixed some of the formatting right away. Notice also that there are 3s on page two, below the staffs, that I can't select at all.

I searched online, and dug through the manual and came up with bupkis.
You all have been great with helping me out in the past.
I sure hope you can point me in the right direction this time because I am at a total loss.