No, do not do that! Open the Tileset in Paint, copy and paste your new tiles over the old ones, then recolour the new tile to for the pallette! It is better than indexing, as you get control over how it is coloured.
No, that isn't the problem (In my experience, that isn't too good). Did you recolour your tiles you wanted inserting with the colours of the Tileset? (Using the Dropper Tool in Paint, the one like the things you take Eyedrops with)
NO RANDOMNESS! It makes the hack seem unbearable "Here, have a Pokedex"... Why?
Grammar - Check it!
Maps - Improve, not natural enough! Also, play through your maps, checking there are no errors (Especially with the borders!
Scripts... Need work.
Tiles - Insert your own! Mine are good as a start point, but you need to add your own!
Cannot access the cave - Wrong entrance on it as well.
Beginning is kinda... Weird.