Auto-tracing your scanned templates may be one part of the issue as it certainly produces huge amounts of paths and anchor points in this case (based on the preview you posted).
If, for some reason, you can't take the scanned raster art as is, you may want to simplify the auto-traced cherry blossoms (Object menu > Path > Simplify). That may help a bit.
Another thing are your .pdf export settings. Can you clarify what you are using there?
And another excellent approach, of course, would be to provide a sample Illustrator file and post a public download link for inspection. So one can have a look at it and see what further slimming diets may be possible.
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