Hmm...technically I made the transition, but I barely changed anything. ^^;
To be honest, I don't see why you should have to 'change' from page format to scroll format, unless you're commonly doing stuff like double-page spreads that just don't work vertically (but honestly, they don't work in traditional 'one page at a time' webcomic format either).
If you do have a simple 'one page at a time' webcomic, I see no reason why you can't just...stack the pages? People will still be able to read it just fine...I mean, that's basically all I did at first, and I never received any complaints.
Then if you want to change how you format new pages, just let yourself go a little bit. Allow your drawings and speech bubbles to take up more space; don't add sideways if you can add below. As the panels get bigger, your comics will naturally extend vertically.
But you can still think in terms of pages if you want to...I mean, since I draw on physical paper, I kinda have to. ^^; For example, this is one 'page' of my comic, DotPQ
It's still formatted traditionally, even in the sense that it ends with a finished bout of dialogue, prompting the reader to 'turn the page'. The only major difference is those w i d e panels: where I once might have fit 6 or even 8, now there's only 3, and just one per row.