Many of the link problems with the tags, categories, post calendar and the comments appear to be fixed now.
The correction was in the Permalink settings for WordPress – I set them back to default and things started working. I am not sure how that lead to breaking things in the first place; however, for the time being I will be satisfied with a working blog.
Still To Do
- Setup RSS feed(s)
- Display my Flickr images
- Minor visual tweaks