The prerequisite chain will look like this:
Power Plant->Ore Refinery->War Factory->Mainframe
Before it was like
Power Plant->Ore Refinery->Mainframe
Although I did not see it alot online, japan can really rush out the tier three stuff pretty quickly, even supers. Not only that, but I've always kinda found the Mainframe and the tier three upgrade kinda redundant (and since it's how I feel, and this is my mod, this is how it'll be

So, you build your warfactory, and then option for the Mainframe becomes available. You will need to upgrade your warfactory once though to access the higher tier units. I think I will implement this through a combination of prerequisites, fake buttons, and the replaceobject module. You start off with the war factory; you can build your tier 1 stuff, the tier 2 and 3 stuff is greyed out (aka you can't build them). Then you upgrade to tier two. The building is replaced by a special version of the warfactory, I'll call it "JapMechaBayTier2" for now (It will have a new commandset the appears identical to the old one). The tier two units will now be buildible. But note; the icons for the tier 2 units in the orignal were fake buttons. This way, (by side stepping the way prerequisites work) you will only be able to build tier 2 units at upgraded war factories instead of every warfactory. Later on when you build the Mainframe, the tier 3 units wil be available to you. They will require both the upgraded war factory and the mainframe to be built.
And then it will work out exactly the way I want it to.[/i]