I like the overall penalties for the various races. I do want to comment on SS and IS though.

SS I think benefits particularly from the arrangement of the game. Weapons expensive and no comms, no trading. This forces more research to occur than in an alliance game or one without forced expensive techs. Which yields bigger benefits to SS than other arrangements. SS also gets to avoid the paranoia that tends to happen to SS neighbors - the neighbors are limited to "two". Of all the game arrangements I've seen, this is one that is rather more favorable for it. Having the best intelligence net doesn't hurt either when other people can't help you out. The performance in the last game suggests that you are likely to get even more SS (and IS as a counter) in this game. Or maybe that's because people who want to play SS look for such games where they stand a chance at all. I've never actually played a game where SS won. But then, I've never played SS beyond toying around

Compare this to say WM and HE. In a diplomacy free environment these races with more glaring weaknesses have a much more difficult time shoring them up through some kind of ally, which penalizes them harder relative to the other non-econ PRTs.

I'd recommend a 10 pt penalty and/or 10 scrapper reduction for SS due to the somewhat more favorable game conditions.

IT has a very distinct advantage with the setup, and has been penalized accordingly. IS could use a penalty closer to 40 points IMHO. They are the race, behind IT, that could most readily and easily move production to the center area. You have mentioned some concern over them and I tend to agree. If you combined it with a SS penalty I think you might level things out a tad bit more.