From what I read in your post, all your doing is manually turning the feed down by hand (correct)?
If that's the case, all your doing is changing the percentage, of the programmed feedrate.
You could (should) change the feedrate a few lines before the program ends (M17,M30). I'ts hard for anyone here to say just where to change the feed, without seeing the g-code your working with.
This is how I tweak my new programs (feed) at work.
1) Run the program & program the feed to what I think is appropriate (sounds like that has been done for you already)
2) Use the dial on the control panel to turn the percentage of the feed down, when needed (sounds like that's what your doing at the end of your program).
3) Make a note of what percentage I had to turn the dial on the control panel to, to get the desired feedrate.
4) Go to the g-code change my feedrate on the appropriate line.
5) Run the program again (new feedrate).
Feedrate programed at 100.0 , lets say I had to turn down the feedrate on the control panel to 30.0 to get what feedrate I wanted.
So the new feedrate is "F30"
The important thing is to make a note of what you have to keep manually setting the feedrate percent to.