I think you are being a little harsh with the statement "and must summarise that this is a bad design"
Absolutly anything you do on a model car, no mater what, has positive effects and negative effects!! It is always a case though of if the positives out weight the negeatives to decide if you run it or not. Also the adjustment makes a big difference to the drive, sure it is hard to get away from the plunge issue, but at least it can be done.
When you raise the gearbox the driveshafts do start to hit the diff nut if you don't have many up limiters fitted. But what I would say is the whole of last year my shocks bottomed before the chassis, didn't seem to hurt too much and to be fair if you are hitting the the chassis on the deck then either it is set up wrong or you are hitting jumps big bumps!! Also, I don't really care if my chassis hits the floor all the time, it is only what it does when it hits the deck, if it carries on fine..great, if not then I will tweak it.
What do I do when I jack the gearbox, nothing!!! If the raising does what I want it to do then I leave it. If I was then going to run the tranny high all the time then I would possible adjust the shims like Paul suggests.
One thing I would say though, is raising the gearbox does give a lot more drive..however, and heres the taking away with the other hand bit, it does make the car a fair amount worse on the bumps.
Highest you also want to raise it is 0.06", don't go any higher or it really will be shocking on the bumps, I would try the 0.03" one to start with and see how it feels.
Like I say I do think you are being a little harsh with some of your statements, raising a transmission is always going to cause something else to be tweaked. Also look out for when it is high you still have enough engagement of the driveshaft at full droop, otherwise you will be moaning again that the driveshaft fell out and it is such a shocking design
Can I ask are you still running the car with the saddles?? From my experience with the car I very rarely suffer from a lack of straight line traction it is only when exiting the turns, especially for tracks over here. Normally what you will find is the car is actually hanging on to the turn too much and then the rear breaks away. How can you sort that, well maybe move some ballast weight to the rear, lower the front inner link, take off the rear Espeed hanger and run one of the stock positions!! Lots of other ways to get traction.
But of course with all of these changes above you will be giving with one hand and taking something else with the other
E.