I installed the shivering isles a while ago and it added a plugin called DLCShiveringIsles then had to uninstall oblivion. After reinstallation, I opened the SI plugin in the cs to find that it was identical to the master file, with no SI content, so i reinstalled SI. now the DLCShiveringIsles is still the same as the master file, while my Oblivion.esm is full of SI stuff. Is this supposed to happen? Now any mod I start based on the master is full of SI things. Was it supposed to happen, or did I mess something up?

if you have done a clean install then everythign is correct. Shivering Isles replaced the original BSA files with the new updated meshes and textures (including the new one) and anything else that was not in the original Oblivion. The Oblivion.esm is dependant on those BSA files, so no matter what, so logn as you have SI installed it will have those meshes and textures and so forth available.
The DLCShiveringIsles.esp is the file that puts all the pieces together to make the playable content, while, the .esm is the library of meshes and textures. If you were to some how extract the SI's .esp only to your data file and not replace the existing BSAs, you could still go to the Shivering isles and play, but nearly every aspect of it would be...wrong. The entire place would be pink and have ! everywhere.

I know the meshes are right and i have played SI since reinstallation, but my oblivion.esm is different from any plugin I have downloaded from players. how do I make a plugin now without SI stuff in it? it actually looks like Icould play SI with only the master file. I checked various SI items in the master file and they are linked to the proper meshes. Everything works, but i do not know how to mod this in a way someone without SI could use and i don't see why there is a DLCShiveringIsles.esp if all of its information is also in the Oblivion.esm.

As I said, the shivering Isles .esp is what the player plays. The .esm contains the meshes, textures, scripts, and other seperate files. The Oblivion.esm archives all the "vanilla" resources into one convenient location for easy modding. Basically the .esp arranges all the rocks, all the monster, all the trees, terraforms the land, creates an alternate worldspace, creates hundreds of NPCs, and so forth that are all dependant on what is in the master .esm.
I just mentioned this in my first post. Everything is correct. If you do not want your mods dependant on SI content, then don't put any in. Just because your .esm has access to the updated BSA files isn't going to break any mods you release. They will only be dependant on SI if you use an SI item. This is because when the BSAs are updated the file paths inside are still the same for every vanilla mesh and texture that is inside those. So when someone uses a mod that was made by a modder with SI installed but no SI content, the .esp will search for those resources in the BSA file. If they are there, then, tuh-duh. If they aren't then you get an exclamation mark.
Make sense?
Basically, you don't need to understand any of that technical who-ha I said, just understand, there is nothing wrong and you may go about modding freely.

All the content for Shivering Isles is in the Oblivion.esm. The DLCShiveringIsles.esp is only there to load the BSA files (a trick they gave Oblivion for the DLCs).

If you want to make mods that aren't dependent on Shivering Isles there are two ways: Use the Oblivion.esm for SI, but just don't use any of the SI assets and it should work.

Or, install Oblivion but don't yet install SI, but do install the 1.1 patch. Copy Oblivion.esm file and rename it to Oblivion_1.1.esm. Install Shivering Isles and the 1.2.0416 patch if necessary. Then you can use Wrye Bash to swap back and forth between the two versions of Oblivion.esm as you work.

Actually, in this case it doesn't. DLCShiveringIsles.esp is almost completely blank. Some people actually rename the Unofficial Oblivion Patch to DLCShiveringIsles.esp in order to gain an extra mod slot. This doesn't affect the playing of the game at all.

oh, well, I never really dived down into it in the CS to see, it was just an assumption based of the current knowledge I had. I'm glad to see most my facts were right though!

As long as you don't use SI content, your mods won't be dependent on SI. Every mod I've released has been made with the updated .esm (i.e. the one with SI content), but none of them require SI unless they have SI content. They all require the latest patch, but so does every mod I've looked at for the past year or so.