The 5.4 will drop in the mustang without any body mods. You won't have to touch the shock towers. You will need a tubular k-member made for a mod motor swap.
My k-member part# (MU-3020 MS w/4.6 Mts $329) and here is were you can buy it.
Anthony Jones Engineering Y2K Member
Oh one more thing. You can keep the A/C. My car has ice cold A/C with powersteering and powerbrakes.