You didn't give yourself anything too game-breaking, but the minium stone is meant to be later game. Unlike other skyblock maps, you need to work for it. No free ride from me. You need to kill tons of enemies to get the shards and kill enough pigmen to get an ingot of gold. You adding in the bucket could shift the difficulty of this, because with one bucket, you can get lucky and have a zombie drop iron, then force rod the empty bucket to iron, make the stone, then transmute a gold ingot down to iron. With a second bucket, you have 6 iron instead of the normal 3.
I'm not really too concerned about the saplings you game yourself, the only issue is you were supposed to get better trees in the Nether (birch sapling) which can be transmuted into any vanilla sapling. The rubber wood only gives 3 planks, but also sometimes drops resin which can make torches. It's meant to limit you early in the game. For food? you're set for food once you get one bone. You can bonemeal grass to get seeds and use another to get a watering can. For this reason, I am fine with the apple tree. And since alchemical use of darkwood causes more damage to the minium stone than normal, go crazy with it.
