About the sharper clouds: every CGI-background was regenerated for the DVD. If you compare the sky of “Naboo by night” between the 480p PAL theatrical broadcast and the 480p DVD, you’ll clearly see that the clouds are not the same anymore. I think that RU08 made the same finding.
BTW, RU08 made an amazing job, his post about TPM is a bible for me!
About the missing frames, I’ll be more precise when I’ll post about the reconstruction.