Gotcha, I'll keep digging if this is something new users are experiencing. It really should've only been the latter fix needed, and even then temporarily. But I'll figure something more permanent.

The Story Arcs page is really just a fancy image on whatever page you designate, with actual story arcs being populated by Mylar. Unless something like Calibre can do the organizing into things like that, you'd need to do it manually. There's nothing theme-wise that would make that not work.

A bookmark popup is actually something I had while I was working on it, I just disabled it for personal preference. I'll add a setting to turn that back on. Checking for a duplicate shouldn't be too difficult either, I'll see what I can do.

And sadly there's no method to get theme/script access to the admin page that I can see. I had an experimental method for a user registration page that stopped working when Admin became it's own thing. That'd have to be a feature added by the dev.
 
And I've got an idea about the issue with the read (and I'm guessing download) button, I'll push out an update soon.

While I'm glad that sorted it, that really shouldn't have been necessary. The malformed bookmark issue shouldn't be a common one, and just replacing your themeScript would've gotten you the fix you probably needed. I'm just trying to make sure that everyone moving forward isn't applying all of my above hacks when they don't need to (or continuing to dig to find the issue if it's more prevalent)

And I'm not 100% what you mean, though it sounds possible.

You're quite welcome, glad it's working for ya!

If you just put // in front of homepageWrap('bookmarks') to comment it out, does it load?

Yeah I realized that as soon as I posted, but of course GitHub doesn't update the raw file right away.

Since it might not fix it, let's try this:

Replace:
initializeControls('bookmarks');
homepageWrap('bookmarks');

With:
if($('#bookmarks .cellcontainer').length){
initializeControls('bookmarks');
    homepageWrap('bookmarks');
}else{
    $('#bookmarks').remove();
}

No problem, I like the learning aspect of this sort of thing. 

Grab the themeScript from the link I gave before, it should now have a catch for undefined Bookmarks that'll hopefully solve this.

Looks like it's hitting an issue trying to handle bookmarks. Under the error, paste the below and send what it responds.

console.log(Bookmarks);

Alright, I know what that is and I think this should fix it.

Download this themeScript.js and replace the one in the folder and try again. If this works I'll replace the zip in the release page.

If you're just getting a spinning wheel, please open your web browser's Dev tools (In Chrome it's Ctrl+Shift+I) and click Console.

Copy-paste the error here and I'll see what I can do.

The above should be fixed now (it was that you didn't have users setup) I think I've tested any scenario like that.

https://ubooquity.userecho.com/communities/1/topics/756-comixology-theme-v2-finally-released