On Harry being a Mary Sue: That kind of depends what meaning you use.
If you mean the self-insertion, I think that's not too bad. Yes, Harry's reasoning is similar to Yudkowski's, but that's kind of the whole point of the fic. It's not like Harry is a copy of EY himself.
If you mean being idealized and overpowered, I agree. The only part so far where things went wrong because he didn't think fast enough or consider all the possibilities is in the most recent chapters.
On it not updating often enough: Totally, but up to chapter 96 will be released over the next few days, so you may want to stick around for a little longer.