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First, I would try to move the drain line in the floor so that it mates with the drain from the whirlpool and you won't have to raise the tub. It may be a lot of work but it will avoid the awkwardness of having the bottom of the tub at a much higher level than the floor.
If you cannot move the drain line, then you need to raise all of the support points for the tub in order to give you the necessary clearance for the drain lines. Typical support points are below the tiling flange around the rim of the tub and at the point where the tub apron meets the floor. (If the whirlpool tub was made to fit into a deck and does not have an integral apron, then the job will be easier.) Call the tub manufacturer -- they will be a lot of help.
Use pressure treated wood at the floor. You will have to tile over the exposed edge of the wood that supports the tub apron. If the tub requires support under the tub cavity, then you have to support that as well. Make certain that the tub is well supported before you attach the plumbing and install the tile. It is a good idea to install grab bars on nearby walls, particularly when you have to "step down" from a raised tub with wet feet.
Don't be afraid to move the drain line. I am installing a tub on a concrete slab which has the drain line in the wrong location. I considered raising the tub so that I could install the drain connection above the slab, but I decided that I didn't want a raised tub. So... I bought a diamond blade for cutting concrete and I cut a hole in my slab so that I can relocate the drain line and avoid having to raise the tub. It required some sweat and a good dust mask, but it was well worth it. I knew that I did not have any water or gas pipes in the slab, so be careful if this is a possibility.
P.S. As Jay J said, God Bless America. Last week I had to drive 2000 miles to get home, and it was touching to see trucks as far away as Colorado headed for the rescue and cleanup effort at the World Trade Center.