Well, you've already got the larger booster (3rd gen yotas), so if your stock master cylinder can't get the job done, then swap it out for a FJ80 master cylinder. The FJ80 does have larger calipers than the V6 IFS minitruck, but I have no idea how it will do with D60 brakes......
But for sure, your best bet (conventionally) would be to use your stock booster with a FJ80 master.
BigMike
