Good idea, about the body lift. I think spacers could also help you out to reduce body rubbing, as well.
I'm going to explain the gear ratio thing in slightly more detail, since I myself learned it the hard way, AFTER the enthusiasm of buying giant tyres (I'm using 15/42/15 Super Swampers) died down for me!
The standard FJ40 comes with either a 10:37 guchcha or a 10:41 guchcha. Your mechanic will probably be able to tell you which one you have genuine fitted in your FJ. This means that your Differential Gear Ratio is 3.7 or 4.1 (after you divide the larger number by the smaller number). Keep this figure in mind, please.
I've posted a Diff Calculator as a picture here. On the extreme left hand column, your wheel size is given. The top most row gives your Diff Gear Ratio.
Now, the colours. Yellow represents economy. Green gives you the best possible combination of power and economy. The red zone represents over powering, which will literally DRINK fuel AND cause excessive wear and tear to the engine. So you want your gear ratio and wheel combo to fall within the green zone, ideally.
If you co-relate your wheel size (35) with your possible Gear Diff Rating (3.7 or 4.1) you'll see that the 3.7 figure is QUITE underpowered, while the 4.1 ratio is still short of the green zone.
To do complete justice to the beautiful 2F engine of the FJ, and fully utilise the Boggers, you need a gear ratio that falls within that green zone. If the owner of the rig is planning on using these wheels permanently, it's advisable to get the suitable ring-pinion combination, or guchcha right. You'll definitely feel the difference.