what SCORE rallies do you mean? They are "races" and I promise you that running an FJ40 on the course in sportsman(it would fit a few other classes too) would be nostalgic for all of 30 miles or so. after that you'd be hating life.
To start, you need a rollcage, and no, a metal tech cage doesnt completely meet the requirements(get the rule book-nothing against metal tech, you would need to add some tube to their design), 5 point seat belts and a fuel cell.
Also consider you need to average about 25 miles per hour over the length of the race course to make each check point before it closes and you get DNF'd, and if you do miss a checkpoint closure, you wont get a finish, since you will time out. Now, I assure you, that is faster than you think. With traffic jams at chokepoints in the course, flats, fueling, driver changes(you'll be needing those frequently) and the general slow pace you'd maintain in a near stock FJ40, you wont make the time cutoffs... And we havent even talked about breakdowns...
Venture over to pirate4x4, hit the desert racing section and see if you can help the pirate guys in the next race. There is SO much more to the race than getting a truck to meet the minimum requirements.
If you have to race a cruiser, build a 91/92 FJ80 and run in stock mini. There you might have a chance of finishing regularly, and once you get the truck dialed in, it will be competitive.