I apologize if this runs afoul some kind of 'necro' forum rule, but this is the most recent discussion of Valkyrie Profile I've been able to find while trying to research if anyone has looked at manipulating Soul Concentration pattern. The last one is circia 2010 in a defunct french forum.
There is an indicator used in other speedrun places for 100% as far as dungeon completion- there is an audio cue/music change that occurs when you have interacted with all artifact chests after defeating the boss. Notably, this means you have to visit Forest of Spirits twice since the first time through, the cue does not happen (a new boss appears and you have to navigate a section you didn't have to go through the first time there). Trying to track items, as mentioned being horribly tedious, is also complicated by the fact not all artifacts are completely unique. There are a handful you can get duplications (Holy Grail and Faim Fenn are two off the top of my head) throughout a run. As far as tripping C ending because of keeping artifacts/not sending characters, you can manually send up an artifact item to gain +1 Evaluation before initiating a cutscene/exiting a location which ends with you returning to the overworld (which is where the 0 Eval is checked for C ending trigger). You can also take artifacts you want to keep first, and then sending the last, as Evaluation does not go below 0 and you will end up at 1 this way too.