As gimlet said, start slow... I remember doing these sort of mods and what I hated most was changing a bunch of things at once, just to have to redo it all again, although I never made a patcher, I always did it by hand and redid it like so.
Here are some ideas to help you out though, some things that I used to do.
Wall of Stone (the spell) - Make it a tile, or knock it in half.
Fields - Tiles
Roofs (for older houses) - Get rid of them
Crates/Bagballs/Candelabras/Barrels/Soulstones/Chests/Secure Chests(gold) - Make passable (I dunno if this is possible anymore, I have been attempting to convert these items to their previous tiledatas)
Bolas - Convert to older style (cannon ball stack), change hue (I did neon green)
Rings - enlarge (For tele rings and such)
Trees - convert to stumps (or something similar)
Clutter (grass/flowers/etc) - remove (same as roofs)
Living tree leaves - Remove (trees in fel are dead thus they have no leaves, however trees in tram based places of life have leaves, converting trees to stumps will leave floating leaves in Tram/malas/etc.)