Are these chunks of rubber the factory body bushings or aftermarket ones, if so what name brand. I installed an aqualu gen II FJ40 tub and used Daystar poly body bushings, they seem to be a little taller than the stock ones, thus giving you a little bit of a body lift. If all else fails, you could try some of the poly bushings. You could also fab up some spacers out of thick walled steel tubing to get the rear of the cab up/level with the front. Hope you can get something from that.
I think minor spacing adjustments are common when installing the aqualu products. I have heard of this from a couple of others who used new tubs. This is more due to old age and shifting of the frame than imperfections of the product. But I would'nt hesitate to call aqualu and question them, they seem to be very responsive. I did a body lift when installing the tub so slight adjustments to the spacers were fairly simple.
i called aqualu and he said that the body mounts for fj45s changed over the years so shiming may be nessesary and to check the alignment of the cab with the bed(if they are parallel). i ordered some extra chunks of rubber for the bed mounts anyways so i cut some (with a sawzall of course) for the cab mount (3 in total on each side) and it looks good.