Some of these changes seem rather too complicated to be realistic or viable, but I like the first two (especially if the simultaneous repops were weekly at least).
Personally, one complicated change I think would be fun would be to replace variance as it currently is set up with an exponential probability distribution. This would basically mean that a given raid mob would have the same chance of spawning at any given span of time (so for example, it would spawn an expected amount of twice in any given seven-day span, an expected amount of 2/7 in any given 24-hour span, and so on), but there are no restrictions on how short or how long the times between spawns are. So there's no such thing as being near the beginning or end of the window; it's just as likely to spawn at a given time right after having just been killed as it is to spawn a week after it was killed. This is a very natural probability distribution and occurs in real life a lot (at least, approximately; it's kind of like flipping a coin every millisecond to see if the monster spawns. Realistically for P99, you'd be flipping a coin every server tick), and I think it would make more sense than having windows as we currently do. Plus, it would be fun to know that there's a small chance that right after you kill a boss, it respawns while you're still looting it
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The implication of using this distribution for raid mobs would be that people wouldn't be sitting around poopsocking at the end of the window because they know it's bound to spawn soon (as they would with the old variance set-up), but also, you don't have the extended variance mechanic which comes with its own set of flaws (as it's currently set up, it reduces the number of spawns, and also, monsters are more likely to spawn if you're in a period of extended variance (I think; haven't read the exact description in a while)).
Actually, applying these distributions to every monster in P99 would make the game a lot more chaotic and interesting, in my opinion, though, granted, not classic.