You can always submit a "glitchless" time to the main leaderboard. Not everyone on there does the same set of glitches, and some people do race without using them intentionally at all. There is no reason not to submit those times to the board.

No, it would not be acceptable for this board to have a Sonic 3 Complete run on here. However, it may be possible to get that game added to the Sonic Fan Games section https://www.speedrun.com/sonic_fan_games

Funny, my last run was 22 days ago, and it's verified...

...seriously though, mods do this in their spare time. It's likely they just haven't had a moment to check it, especially since it's not a crazy short run. I believe SRC rules are give it up to 3 weeks. They'll get to it as soon as they can.

I believe it comes stock with Livesplit. It should be under Edit Layout - Add - Control - Manual Game Time. I don't remember having to download anything extra, though I could be mistaken.

There is a component in Livesplit called Manual Game Timing that allows you to enter the time instead of running an RTA timer.