Normally, the aftermarket drive shaft flanges are slightly thicker than the stock drive shaft flanges. This may require slightly longer bolts. Get yourself a set of these 10mm flanged bolts to go along with your new drive shaft. Sold in sets of 4, you will need one set for each end of your drive shaft. Some vehicles use studs instead of normal bolts at the transfer case, in which case you won't be able to use these bolts at that end of the drive shaft.
These bolts are now included with any new Tom Wood's Toyota drive shaft.