number one problem is you don't have a body lift as you stated. if you were to chop the floorboard to gain clearance and raise it up you might loose your passenger rear seat and possible something else...cant remember fully everything that's in the way. unless you have a problem with loosing a few gallons of capacity. you could just just let it clearance itself. i know it soudns ghetto but a lot of people with runners just let it get bashed up. it will usually at the most go up 2 inches and that's it. on my runner i lost some carrying capacity but in the end it looked just like a truck would...about 2 inches higher. so far Ive never heard of any problems from letting it do that (like fuel pump breaking or hole in gas tank)
probably not what you wanted to hear but just through id throw it out there.
you could convert to an f150 tank and put it where the tire carrier was. works well with a runner but that also involves some mods.