If I have understood you correctly, you can use the “Paste Attributes” function. Start with the last clip in your sequence, adjust opacity, position and scale for each layer until satisfied. Then copy the clip on the first layer, select all clips on the track (TT on your keyboard) and Paste Attributes (alt-V). Repeat for the other layers.
If you have Photoshop, you might consider doing the layering there and import the file to FCP.
Another thing: If your sequence starts with one clip with 100% opacity, then the next with two layers, the top having 99% opacity, it will look like a cut for the first few clips…Is that what you want?