I usually start off my mods with the tileset. Take a few breaks and work on the other items. Then from there I work on the main menue stuff and eyecandy. I usually test about 50 times up until now, and come up with 3-5 maps to test the tileset. Its not really that hard to do.
If you want some steps, I could give you some (but you may not want to follow):
1: find out what you want the mod to be on
2: start off the tileset with your first ideas on blocks (I find then you can get more ideas off of them)
3: once you have writers block (or moders block) and you can't think of any more blocks, edit the interractive blocks (based on your theme)
4: once you are done the interractive blocks, replace all the original ones (scattered throughout the gfx folder) with the new ones. If using MSPaint, you may find the sketch&screw box to be helpful (for the smaller blocks just make it 50x50 and it will go from 32 pxels to 16)
5: work on the tileset more (you probably have more ideas from thinking, researching, and working/playing)
6: work on the shells and other items, edit them so they work with you're theme
7: if you havn't already, delete ALL the maps (except the ZZLevelEditor one, you will need it) and all the skins that don't have to do with your theme (keep at least 1 so you can test)
8: make a map with the tiles you have already. Since you have only been working on the 1 tileset (I hope) the map preview will look pretty screwed up. Don't worry, and test the map
9: make any changes you found from playing the map
10: now make more tiles, or work on the menu
11: in the menue, you can either design your own menu background, or just replace the BG with a map BG
12: now try working on the awards. Replace all the shells and stuff with the newer ones, and edit the boxes to fit your theme
13: edit the mod objects to fit your theme
14: now stop with the packs folder, and work on the leveleditor one. Edit all you can there
15: now in the docs folder, you may find many objects you have edited, fix that. Open them up, and past it in (size it) and save over it. I just ignored the SS
16: back to the tileset. Work as much as you can on it, as its one of the few things left (in comparison)
17: if you want to change the fonts, here is a good time. You don't have to, but you can (makes things harder I find)
18: powerup could now use a change. Edit all the mushrooms and items to fit the theme
19: now that the items are changed, now you may as well change the projetiles to match the item
20: mode skins should be changed now, if not earlier
21: BG can be changed now, but I suggest that you focus on finishing all the other folders that are not complete (you will be moving on to different foldiers)
22: if you want, change the backgrounds now. You can always come back, but for the sake of the mod, change them now, so you can forget the gfx folder
23: I didn't bother with the retro folder, so move on the the music. Change the main menue music to the main theme music of your theme
24: change the battle musics with other music from your theme
25: if you think the music is good, then move back to the tileset. Fnish it if you are not done, then size it and paste it in the other tilesets, then save over. Now the map previews should look like the maps
26: Delete the tours in the tours folder. All the maps will be scrwed up, so don't bother keeping them. Just save 1 so you can open the game (if you have none, the game may just crash)
27: now work on anything you want in the sfx folder. The only thing that you should want to change is the announcer (you don't need one)
28: the time has come for you to become a map specialist. Make maps, many maps. I would say 25 is too much, but 10 is too little
29: tour time. Make a few tours that follow through the maps (each tour should have a theme within the mod theme)
30: if you think everything is done, you may announc the finished completion to the forum. If not, fix the stuff up so you can release it. PLAY EVERY GAME TYPE TO MAKE SURE THAT YOU HAVE CHANGED THE MOD OBJECTS! Be sure to add in the credits box "Mod by: [insert name here]", but ensure you give credit to those who actually made the game itself. You just get credit for the mod.
Note: this should take a few weeks (if you work really hard). Try and take your time, so you don't have some stupid mod that no one will want to play. Take some days off, and work on other thing you want done in your life.
Other note: you don't need to follow my steps step by step, you can mix them around, or completly ignore some (bad idea). Also, don't ask me for what the filter folder is about, as I don't know.
I hope this all helps. Have fun, and don't be afraid to ask for help if you need it. This may not cover all the things, but I know that it covers most. If any other people think I forgot something, TELL ME PLEASE!