I'll try to catch up here.
Alt-J: If Ruff meant he added Alt-J so it opened the same options screens as Ctrl-Alt-O, fine. If not, I'll add it.
Specialist Stacker: It actually hasn't been included yet.
You're seeing the vanilla specialists. It's "on my plate."
The icon issues: The reason some icons work and some don't is because there are two fonts (different sizes). It seems that one of your font files is either corrupt or missing. You should have a gamefont_75.tga in CustomAssets. Try removing it temporarily and see what happens. You should see all icons except the Attitude Icons in the scoreboard (that's all that has been added). I can't think of a reason why this doesn't work for you, but I'll say that since it fails in Warlords the same way, it's likely your installation is just borked. Get your CD back and reinstall, sorry.
Pillaging Roads: That it happens only sometimes that you pillage roads is rather confusing. It should happen every time as I guess that the code is grabbing the ImprovementInfo for the improvement that was pillaged, and roads don't have one. Thus, it's trying to ask "nothing" for a description -- rarely a good thing to do in code.
I'll take a look. It should be easy to fix if that's the problem.
Alerts: I haven't gotten to this. Hopefully this weekend.