1) You have to re-run MassReplaceIt every time you publish. I wish there was a better solution but there isn't. I hope you saved the query so the next time you only have to hit Replace in MassReplaceIt without you having to re-add all the Find&Replace every time. I'm sure you will get used to it. Of course it would be better if iWeb featured a better way to add HTML than HTML Snippets but that's something you have to blame Apple for.
2) I don't know about that, sorry.
3) I guess you could achieve what you want with adapting this:http://iwebfaq.org/site/iWeb_Hover_photos.html
to your needs. Instead of a thumbnail use a transparent image you put in front of the text or have the text on the thumbnail or you could also use text as the link like
<a class="photo" title="Name">This is your text<img class="big" src="http://iwebfaq.org/images/gallery1.jpg" /></a>
when people point the mouse over "This is your text" then the image would change/display on the other part of the page.