If you're having problems with links not woring because the index.php is dropped, I think I figured it out. I don't have mod_rewrite on my host, so I can't use permalinks and none of the other non-permalink options would work consistently for all links. For others in the same boat, here's what I did.
In the following files, replace all of the "/?" (without quotes) to "/index.php?" (without quotes)
In this file, replace this line (line 32) "$catlink = $file . '?cat=' . $category_id;" with
$catlink = $file . 'index.php?cat=' . $category_id;
I haven't found any issues yet, but I haven't thoroughly tested it, either. If there are some issues, let me know. Maybe this could at least lead us in the right direction. You can see it working here: http://www.jeboothjr.com
This is gonna at least let me get my blog started. I hope it can help somebody else out, too.