I'm not aware of splitting the MiniTOC in two columns. However, I'm familiar with a technique where you create a two column table (no borders) with a narrow column on the left and place the MiniTOC there running down beside the Topic text which has been placed in the right hand column. With frequent "Back to Top" links, this can be a very handy way for the user to navigate a long topic. (This works in a CHM as well.)
Willam van Weelden, our resident scripting and css expert is pretty busy now, but he might chime in with some thoughts on this.
Other than that, if you have a hundred(!) I'd be inclined to seriously rethink the length of the topic :-)
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Just a possible suggestion for a workaround. I know the Mini TOC is incredibly cool, but something like this requires a bit more effort and "thinking outside the box".
One thing you could do would be to insert bookmarks at each heading you would link to. Then insert a Related Topics control that points to all the bookmarks. Configure the control to display in a "Topics Found" window. This would provide a reasonable window presenting all the links to the bookmarks.
Following on that same stream of conciousness, you could also create a table at the top of the topic and insert links as you want to see them in separate colums.
I'll close by strongly suggesting you file a WishForm to ask Adobe to enhance our customizing options for the Mini TOC. (Link to the form is in my sig)
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It's sort of possible to code a hack for it in your stylesheet, but I can't get it to work in IE (8 or 9) - so probably not really useful and no guarantee it would work in multiple version of RH. But I'll post in case anyone is interested. The most recent copy of RH I have is RH8, so this may not be true for RH9.
In RH8, the output creates a div for the mini-toc, and the ID given appears to be prefixed with MT, so I used some CSS3 selector codes to apply this to any div with an ID beginning with MT. Then the rest says display in 2 columns, and try to spread the content of the div evenly between the columns. The first 2 lines work in Opera and are the "standard" names. The -moz- lines make it work in Mozilla based browsers and -webkit- makes it work in Chrome based browsers.
-webkit-column-fill: balance; }
http://www.w3.org/TR/2011/CR-css3-multicol-20110412/ - new css3 column coding, but not yet finalised.
http://msdn.microsoft.com/en-us/library/ms531207(v=VS.85).aspx - MS supported CSS properties
http://peter.sh/experiments/vendor-prefixed-css-property-overview/ - vendor prefix properties