I have a 98 flareside f150 with a 5.4 trition and its two wheel drive, and just purchased a 97 f150 4.6 thats four wheel drive and has a blown motor.

I was wondering if it would be possible to swap the 4.6 with the 5.4 triton. Im hoping to make a nice offroading vehicle. I'm pretty sure it would mount up correctly but the other question i have is will the computer from the 4.6 work for the 5.4 im intending to swap or will i have to get another one?

 

Yes it will work. Check out this thread.
4.6 to 5.4 Swap Notes - F150online Forums

What are you doing with the flareside after you take the motor out?