Okay, how do I increase HP and AP limit of player characters beyond 999?
Don't know if it is the case for this game but usually points like that are coded to use a value of a given length (if you have ever seen the 128,256,512,1024 progression in things and wondered why then consider what each of those, or one less than, represent in binary).
Certainly you can increase the length but you then also get to track down all the things handling those values to make sure they know to use the larger format (every stat, battle and whatever calculation, including other calculations it gets involved in*), all the things displaying it, and possibly the save format and handling for it.
*if a game adds values together in something then keeping both components at say half the max means even at the limit things still add to underneath the max.
On rare occasions you might be able to bump things up to the limit if they say round to the nearest 100 (1024 takes 4 characters on screen but 999 only takes 3, technically then leaving 25 values extra available) or maybe even something really small like 50 to limit overpowered things in play. Whether this minute extra helps will vary with the game -- I have played games where it is ultimately meaningless, and I have played games where because of exponential growth the extra 25 levels or something changes things radically. Many game devs go more along the lines of "eh, works OK" some devs do balance things out (or balance things within their expected parameters.
In any case this is not normally the sort of thing I expect to see in a ROM editor. Maybe the occasional save editor will put your item values over a limit for you (hopefully the game does not put them back at the limit).
Of course you can always go the other way and half the cost means double the effective mana or action points. Half the damage is double the HP. Reduce the stats of enemies and you have functionally the same effect as increasing your stats.