I also convert my comic to vertical scroll format!
Took a while to figure it out, especially because I tend to have quite a bunch of horizontal panels and I don't really like the idea of rotating panels, soooo... here's what I do:
1 - Like others above, I make my comic in page format first. Mine is on an A4 sized canvas at 300 dpi, which then gets resized at 940 x 1330 pixels for ComicFury and my own website:
The lettering for this version is done in Clip Studio Paint, save for sound effects, which are usually done in either Photoshop or Affinity. At the same time, I make sure to also save a full size version of the page WITHOUT balloons:
Since I'm going to re-letter the whole thing for vertical scroll format, having a lightweight file with no balloons makes it easy for me to copy and paste the panels
2 - Vertical scroll conversion! For this, I use an 800 x 5000 px canvas in Affinity Designer. I use 800 pixels as my width because that's the maximum Webtoon will allow, and since I don't want to clutter my pc with too many versions/sizes of the same page, I just upload my comic at the same width on both Tapas and Webtoon. As mentioned above, this version gets its own lettering. Pasting balloons with the original lettering would cause inconsistencies in font size when resizing the panels, so I prefer to redo the whole thing from scratch instead. This also allows me to ignore some of the constraints that the print version requires, like balloons going out of the panels:
Basically: I select the panel without balloons, paste it into the vertical format page, then redo the lettering. If a panel is too wide, I tend to split into into multiple panels. For example, this panel here:
Looks like this in vertical form, with the long horizontal panel split in two:
I don't do a whole lot of gradients to connect panels unless it's pretty easy to include (e.g. the original panel already includes a view of the sky or some magical effects):
And sometimes, I use lettering/effects to connect one panel to another:
It IS a pain in the butt, but... doable, I guess? 