Sorry to jump ahead in the order, but I recently (read, yesterday) sorted my folder of Marvel Comics Presents (1988 - 1995) and noticed that not only does it contain anything up to 5 stories per issue, but sometimes the order of the leading story will change from issue to issue, or a new story line will be introduced with the final story of the ongoing one.
If you don't mind my asking, how do you intend to present this in the order list?
Marvel Comics Presents Vol 1 #024 - The Retribution Affair, Part 08 - Retribution And Resurrection (& Others), Pharaoh's Legacy, Part 1 - A Change Of Heart
Marvel Comics Presents Vol 1 #025 - Pharaoh's Legacy, Part 02 - A Heart Reborn (& Others)
In this case, Pharaoh's Legacy would be 024d in the first one, but 025a in the second.
Marvel Comics Presents Vol 1 #160 - Origins, Part 01 (& Others)
Marvel Comics Presents Vol 1 #161 - Smells Like Teen Spirit, Part 03 - Yesterday Will Be More Fun Than Tomorrow (& Others)
Marvel Comics Presents Vol 1 #162 - Slave Of Passion, Part 01 - Ensnared (& Others)
Marvel Comics Presents Vol 1 #163 - Smells Like Teen Spirit, Part 05 - Time Wounds All Heals (& Others)
... where Origins, Smells Like Teen Spirit, and several others are running concurrently, but switching position within the comic from issue to issue. I've been debating opening the rar file and separating the stories and renaming every one for ease of access corresponding to the order, and hence a look into what you intend to do is of interest to me.