So I did try using the website to change. It would only let me change the same day and there was only the one flight available (the one they already rebooked me on).
Any time I tried to do different days/etc. it would give me an error.

I called back again and got another agent.
She had difficulty as well.

I basically had to go through 4 different cities/dates and have her read me each "available" itinerary which was either one flight only or red-eye only.
But when she tried to book me on one that was supposedly eligible, it wouldn't let her do it either. I could hear her say, it's an I-fare, it should let me do it, why isn't it, etc.?
After about half an hour she said the system wanted her to CANCEL the existing booking, reissue the certificate and THEN book a new flight, which she said, "not doing that" (we both know what happens then).

She finally basically said she'll do it a different way (in other words, screw this, but she did NOT say that) and did an "even exchange" and even switched to a different originating city.

I think in all my years of using the companion certs, I've only ever had it work online (or changing, etc.) twice in 10+ years. Every other time, it's given an error (even on the flights it claims are eligible) and I've almost always (90%+) had agents on the phone fine more flights than delta.com shows.

Anyway, back to the Matrix (haha):
Is there a way to get it to construct proper fares? I don't believe any of the options it showed had more than 4 hours in between the one connection.

It would just be nice to be able to find something (alternatives, etc.) without having to spend 1+ hour on the phone with an agent (not counting hold times, etc)
But there may not be a way to do this.