I have the 54 gal. Transfer Flow replacement fuel tank on my '98. 5 LWB QC 4x4. I realize you are talking about installing one on a 4x2 however, I thought I might step in and give some perspective. The front, bottom edge of my tank is just slightly higher than the OE skid plate. With that, I'll bet you 4x2 guys don't have a skid plate right? Oh well.
Anyway, suffice it to say, yes, the 54 gal. replacement tank does hang down 2-3 inches farther than the OE 35 gal. plastic tank.