Tourweaver 6.5 doesn't support pop-ups.
Tourweaver 7.0 does support pop-ups.
File size in doesn't matter for HTML5 because Tourweaver only outputs iPhone images sized at 500px cube faces and iPad at 955px cube faces. You can confirm this by checking your published HTML5 scene folder.
Understand HTML5 is an inferior platform to Flash and not all features work.
Please see the HTML5 section of the (F1) help file.