Hey gozmoz--I might need a little more information from you in order to help here. It sounds like you've got potentially THREE different homepages (see below). First of all, is that right?
1. example.com
2. example.com/index.htm
3. example.com/index.php
Big red flag to me is the Wordpress plugin you're using that automatically appends .htm to the end of every URL you've transferred to your new WP CMS--why were you unable to keep the URLs as-is, without the .htm? My rec here would be to undo that, and keep the original URLs (without .htm).
**Question 1: **As far as this question goes, I do think you'll need to clarify the above before I can make a solid rec for you. Again, my preference would be for you to use your original URLs as the main ones and deprecate these .htm versions if possible. That _may _require you to 301 redirect the .htm versions to the non-htm counterparts.
Question 2: what do you mean, example.com/index.htm no longer exists? Have you deleted this page entirely? If so, you may not need to do anything here. I do however, think you need to establish a singular URL to be your homepage, and see no reason you shouldn't use example.com (on its own) as your home, instead of appending /index.htm or /index.php