Just to add, I got into a bit of a kickstart on the rest of them as well, here is what I have since my last post:
Enhanced Briefing Text with $h and $f as appropriate
Removed additional or unecessary line breaks.
SM1-01.fs2
Added Alternate Types: NTCv Deimos & NTF Hercules
Removed Prometheus R & Akheton SDG from Weaponry Pool.
Renamed all Tag occurances of "Psamtik" to "GVD Psamtik"
Replaced "Subach HL-7" on all Vasudan Serapis to "Mekhu HL-7"
Renamed all Tag occurances of "Belisarius" to "NTCv Belisarius"
Added "$Alt: NTCv Deimos" to NTCv Belisarius
Nameplate Texture renamed to NTCvBelisarius & updated
Added "$Alt: NTF Hercules" to all NTF Fighters
Added "( tech-add-ships "GVF Serapis" )"
Removed trailing ";;FSO 3.6.9;; $Bitmap List:"
SM1-02.fs2
Added to Alternate Types:
NTF Cargo
NTF Hercules
NTF Loki
NTFr Poseidon
NTFr Triton
NTSG Alastor.
Removed Prometheus R & Akheton SDG from Weaponry Pool.
Added All "$Alt:" tags under $Class as appropriate.
Corrected Message name & reference to "All Fighters detroyed"
Removed trailing ";;FSO 3.6.9;; $Bitmap List:"
SM1-03.fs2
Corrected Alternate Types:
NTF Fenris <- Removed
NTF Leviathan <-> NTC Leviathan
Removed Prometheus R and Hornet from Weaponry Pool
Renamed "Iceni" to "NTF Iceni" and updated all Tags
Corrected all mis-spellings of Iceni as "Icini"
Renamed "Glorius" to "NTC Glorius" and updated all Tags
Renamed "Impervious" to "NTC Impervious" and updated all Tags
NTC Impervious $Alt changed from NTF Leviathan to NTC Leviathan
Corrected all mis-spellings of Impervious as "Imperious"
Renamed "Psamtik" to "GVD Psamtik" and updated all Tags
For +Name: Rebels Armed, correctly set beam-free-all for NTC Glorious
Glorious Destroyed message handle changed to "Glorious Down" to match "Impervious Down"
Each multiple instance of "allow-weapon" now nested once rather than repeated.
Removed trailing ";;FSO 3.6.9;; $Bitmap List:"
So far, all of these are probably extremely trivial and don't really "fix" anything (but at least they also do not break anything!), but were more of a "I noticed them, they bugged me, I made them go away".
I'm still working on the training missions, because their behaviour is not entirely consistant. In the first one, you get yelled at if you don't match speed the first time, but any other objective you can just sit on and do nothing. Also, once it clears you to return to base, it doesn't care if you fire on the instructor, which should still be on if you have not left yet.
I am a tad leary about overly modifying these away from the original mission files, but I _am_ ensuring that any changes that I make also work under retail. (Which, let me tell you, makes me appreciate running the SCP +MediaVP's the more I test.)