The scrolling issue is caused by a bug in ClickFunnels.  I've included something you can paste into your Custom CSS setting to fix the issue.

.containerModal { position: absolute !important; }

This will work okay with popups ABOVE the fold, but may cause the buyer to have to scroll back up the page if you have buttons that open the popup below the fold.

Another simple way to fix this is to remove the Custom CSS that you just added.

Then add content to your popup that will make the initial state taller than the screen like Step 2 is, that way when the page first loads, ClickFunnels will see step 1 is too tall and make their regular adjustments to make it work.  Then step 2 will be good to go as well.

One way great way to do this is to add something like Trust Seals like you see on the Dot Com Secrets and Expert Secrets book funnels.  That's extra content that will make the height taller.

Alternate CUSTOM CSS you can add to your page is as follows:

#modalPopup > div.containerInner.ui-sortable
    width: 720px;
    height: 100%;
    position: fixed;
    background: #fff;
    z-index: 1;

This code snippet will create a fixed popup modal with a scrollbar.   You may need to alter the selector and/or the width pixels to match your needs.

Note:  This may not be mobile responsive after adding this code.