Never heard of that site before. Will have to have a look around it later.
Games with different update levels can make mods tricky. I will note also that if you can get the mods working by selecting the appropriate update level then you can use those to gain some insight as to what you need to change in the future -- unless the updates specifically mess with the thing the mod targets then chances are you only have to find where the new location for the relevant code/data is.
Most of those are likely to be fairly basic tweaks on equally basic cheats.
Tool durability is likely to be no different than infinite health, infinite mana, infinite money, infinite potions or the like to find. That is to say get a tool (maybe make it a late game fancy one/high durability one if there is such a thing), use it such that durability goes down, search for changes, repeat a bunch of times until you find it, maybe do nothing and search for things that stay the same to eliminate background timers/animations/... that might also change RAM.
From there you can either add something to the durability counter (assuming it is a simple number rather than number of hearts or something), a basic cheat might even be able to be used (if it is normally 30 then injecting 120 or doing a shift, shifts tending to be why multipliers are involved -- shifting in binary is much like multiplying and dividing by 10 in decimal in that you "shift" the decimal point around), or reducing the damage taken if that is a calculated effort. Alternatively if there is a table somewhere in the ROM, or a durability rating within the tool definition, then yeah you can edit that like any other stats.
Increased stack could be marginally more tricky. Start by finding a have infinite cheat for some of the items in question. Items tend to play out in two, maybe three in the modern world, ways.
1) Items in a big grid/list that correspond to their counts that the game knows to look up (think big spreadsheet).
2) Items have identifiers and are still in a big list (50 of item 1, 2 of item 4, 16 of item 11...)
3) If the items are crazy custom then probably still a big list but each thing is more likely to have individual flags and modifiers internally (think what XML is used for). You won't find this in a 16 bit RPG though. You might also have something like this elsewhere in the game to indicate what can be traded, similar to how you might have weapon stats and what party member/job type can equip it be a separate thing to how many of each item you have (the stats won't change but the amount you have, and consequently how much data you need to save it, will). You might also be able to go further than that as part of said flags is likely to be whether it is stackable.
There are indicators of what it might be from within the game -- if you can arrange your bag or have a limited amount of items types within it tending to be an indicator for 2) above but not always.
Start with an easy to get item (maybe make infinite money and go to the shop to buy things/sell things) and then move sideways.
It might be that a cheat to give you more items than normally exists in the stack just works (at least until you get below it*) or the game might have some kind of catch to force it down.
*bit of a cheat but if say 30 is the limit then where the game might do if item count = 30 then don't allow any more, and as you can only get one at a time that limits things conventionally, as 31 does not equal 30 it will allow you to carry on. This means a cheat along the lines of if item count = 29 then set it to 31 will dodge the issue without having to delve into code.
3. Possibly more tricky, or at least I don't have an easy way to go about this without delving into assembly.
Start by finding infinite money (or whatever currency the boat ride uses). You will want to set a breakpoint to find what instructions edit this. Pay for the ride and the breakpoint should flash up saying something tweaked it (it will also do it in shops and whatever else so be aware of that one/stick to the area you care about for this). Now many things could tweak it and it might even be a money handling function within the game, however somewhere in there will be the value it deducts. Work backwards from there to find where the value is located (hopefully it is directly there as an immediate in the code but you can only be so lucky).
If doing it as a cheat you might be able to do something like find an indicator that you are in the boat ride section that is not present elsewhere in the game. From there you could have it watch for a drop (presumably copy the money value to a stored location and compare it to things, it dropping by say 30 which is the normal cost of ride in this scenario would then be able to be have 15 added back in. Makes it tricky if the game needs a minimum cost to ride despite having apparently less cost, though the same could be true of the assembly method in that you need to find the minimum as well (though if you can handle assembly for the first you can handle this well enough as well, albeit it will probably be a break on read you use rather than break on write).
