I like this! Here are my change suggestions.
When skipping a board, don't add the timer value to the score: I think it's much better to skip boards and keep the score "clean", adding up just the points that have been earned. (IMO, you do not earn the bonus timer until and unless you clear the board.) Or, it could work such that you won't get the timer bonus added if you skip the board during the stacked monkey screen, but will get the bonus if you skip it with the playfield on screen.
Automatic Free Play: This trainer will never be used in a conventional on-location setting, therefore credit-handling tasks are probably a waste of memory and time. Just simplify and make pressing 1P start the game.
Remove the intro cutscene: "I want to see that intro again!", said no one, ever. And look, more ROM space!
Reset the hammer score upon grabbing a second hammer: Individual hammer points are much more useful than cumulative hammer points for the board. For the first hammer this is no problem, but if you want to know how many points the second hammer was worth, you have to remember what the first one was worth, then subtract.
Change the input triggers: "tap for function 1, longer press for function 2" is awkward. The problem is that to get the secondary function you have to press the button long enough to not trigger the first function, but if you press it for too long, you'll trigger neither function, and if you press it for 3 seconds, you'll trigger the third function! So getting all of the functions to trigger is actually a bit of a skill in itself. Suggestion:
1P = board replay
2P = board skip
Jump+1P = speed down
Jump+2P = speed up
Reset to attract mode = Jump+1P+2P
Speed reset = drop it. Easy to reset it to 100% with the J+1P=down/J+2P=up method.
5-1 Warp: For a trainer, it can't be emphasized enough how valuable it is to be able to skip all the early levels and go to 5-1 instantly, since that's the beginning of the real game. With MAME, a 5-1 savestate can be made as a workaround, but if and when this becomes compatible with arcade hardware, anyone who wants to practice internal difficulty 5 will have to manually skip the first 14 boards every time. I suggest assigning a specific trigger to warp to 5-1. Perhaps 1P+2P? Or, you could even make it a dipswitch setting, replacing the "extra life at" switch (which is pretty useless) with a "start at Level 5" on/off switch.
Add a key to the high score/insert coin screen: remove the Insert Coin stuff, then use this screen to describe what each indicator shows, and what the button actions do. In-game documentation would be good, otherwise users of this ROM will be dependent on the DKF thread for an explanation. A few things, like the blue pie, will be a total mystery unless explained.
That's all I can think of for now!