About three different homepages: This is my reasoning: Wordpress based website uses index.php as a home page if you use "latest posts" as your home page, Even index.php is not displayed in the url address bar. Does that mean WP sites always have 2 homepages? I have removed index.htm at the moment, but I see that as a problem as I am losing PA value for that page.
Zee: So it sounds like you should create a "dynamic" front page (this link should help you: https://codex.wordpress.org/Creating_a_Static_Front_Page). If for some reason you are unable to remove both duplicate homepages, I'd say deprecate one and 301 redirect it to your main homepage, and implement a rel=canonical tag from the duplicated homepage to your main one (e.g. example.com/index.php -301-> example.com)
I can see that this is a bit messy.. I did this as I wanted to preserve
original htm based site URL's. Are you saying that search engines see
www.example.com/dir1/dir2/page.htm and www.example.com/dir1/dir2/page as
identical URL's.
Zee: I can't say for sure, without seeing your site, but if they're indexed (discoverable by search engine crawlers), you could definitely be penalized. If your .htm pages have built up link equity, you'll need to 301 redirect them to their corresponding pages
With my old htm based website I had too many subdirectories. I have
removed some of the subs to make URLs shorter and used 301 redirects in
.htaccess file. I probably should have removed .htm appendixes as well
at this stage, but I did not.
Is there a point to do 301 redirects again? 90% of my pages have been 301 redirected as I have removed some of the old subdirectories. Are you saying that I should again 301 redirect my newly 301 redirected pages?
Zee: No, that'll result in a 301 redirect chain--you should ALWAYS 301 redirect to whatever the most appropriate, final destination is (think of 301 redirects as nonstop flights, never layovers). If I 301 redirect A --> B, but then B needs to be redirected as B --> C, you must update A's to reflect this as well, A --> C, to avoid a redirect chain.
I would like to use example.com as my home page only, I am just trying to transfer PA value of my index.htm page to example.com. Not sure how to do this.
Zee: You may want to canonical this one, in that case (especially if you can confirm that these pages present the same information)--you can implement a rel=canonical on your .htm homepage that points back to your main homepage.