1. Make sure you .exe file name is 12 chars or less when you publish. And for safety, no spaces or special characters except maybe underscore. Easypano is fixing the 12 char bug.
2. My .exe is 40 MB that runs fine.
3. I don't have nearly that many links or hotspots or popups. I have have about 150 scenes (some just accessed via thumbnails for now). So don't know if your problem is caused by large number off links, hotspots, or popups... but I am very interested in large numbers like you for my clients.
Hope this helps a little.
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