The sequence is very short, maybe 30 seconds, but having it all in AE will let me create the transitions I want to do faster than making multiple compositions within the Premiere Sequence. I don't want to import the years long project into AE, just a single short sequence. But when I try this it wants to imports all of the footage within the project versus just the clips I'm using in the sequence.
Importing a Premiere Pro project will always bring in all of the footage in the project after you have been given the option of selecting a sequence. This actually makes sense if you assume you may want to change something in AE which is the reason you probably wanted to import the sequence in the first place. There is a workaround. Reduce the project in Premiere Pro.
Here is how: Select the sequence you want to open in After Effects in the Project panel in Premiere Pro then go to File>Project Manager using Premiere Pro's menu.
Inside the Project Manager, you should see only one checkbox selected in the list of sequences. Check the appropriate options. There is no option that does not include copying footage or transcoding footage and moving it to a new location. If you have a bunch of mixed formats I would suggest you choose to transcode and pick a suitable standard production format from the list. Exclude unused clips and include some handles so you have some room to work. Then create the new PPro project and copy the footage to a new location. This is the only way you can get After Effects to import only the footage that you have in a sequence when you import a Premiere Pro project into AE.
The only other option is to use Dynamic Link and select all or part of the shots you have in your sequence, right click and create new comp from the selection. You will have to fix dynamic link first and that may involve transcoding some of your footage. Personally, I do not think this is a very good option for your project even though it is only about 30 seconds long.
Please pardon a cautionary tale. I am not trying to throw water on your project. Most of the time fancy eye candy transitions detract from the story you are trying to tell. Be very careful with your choices. You almost never see anything other than a cut in a dramatic film or commercial. It is time for the story.
In late 1990 I was running a production company and I purchased a Video Toaster because I saw it at NAB and it was all the rage. Quad Splits, a zillion wipes, text effects and other eye candy. We made less than a dozen commercials using it then I sold it because the commercials were not working as well as the ones we were making before with nothing but cuts and an occasional dissolve and the clients we had quickly got bored with the gizmo. The fellow I sold it to used it for about 2 years and then moved it to his basement where it probably still sits. It is not that it didn't make all kinds of really great eye candy, it is just that the eye candy did not help either of us tell an effective story.