UPDATE: Slight progress. Still not completely back, but almost. Comments can be had, but you cannot see them from the main page. If you want to comment or read comments on a post, click the "time stamp" at the bottom of the post, that will give you just that post and from there you will see "comments."
Being that I have been using the same template since '04 and it no longer supported a lot of what I wanted to do - this little awkward stage will be worth it. Sure, code is art, I guess, but it is still ugly.
Be patient, I'll get there. Today is that final day of MilBlog silence for CJ - so regular posts start again tomorrow.
UPDATE II - Electric Boogaloo: You can also access comments, indirectly, via a reply to the comments on the recent comments gadget to the right.