Truly odd, I've downloaded bunches of Mike Stone's planes and have not had a similar problem - his are usually trouble-free. Anyway, open the aircraft.cfg file located inside your main C-141 aircraft file (open with MS Notepad), and look for entry for Contact Points. You will see something like below, which is in fact copied from my own C-141 that comes from a different source:
point.0 = 1, 52.40, 0.00, -10.00, 5000, 0, 1.500, 80, 1.0, 0.9, 0.9, 5.5, 5.5, 0, 0, 0
point.1 = 1, -12.70, -8.50, -10.90, 5000, 1, 1.500, 0, 1.0, 0.8, 0.8, 6.9, 6.9, 2, 0, 0
point.2 = 1, -12.70, 8.50, -10.90, 5000, 2, 1.500, 0, 1.0, 0.8, 0.8, 6.5, 6.5, 3, 0, 0
static_pitch = -0.95
static_cg_height = 10.60
gear_system_type=1 //Hydraulic
point.0 is the nosegear, point.1 and point.2 are maingear. Scroll along to the fourth figure in each one (for point.0 above, is -10.00, and for point.1 and point.2, is -10.90). To make the gear appear closer to ground, reduce this figure, try adding a foot at first (e.g., -11.00). Increasing it brings the gear closer to the fuselage. Save your changes and give it a go, this is a trial-and-error process. Always make a backup of the original aircraft.cfg before doing any alterations.
EDIT - Just reread your post and didn't factor in the fact that the nose gear is OK. You can also try adjusting the static_pitch factor, maybe try 1.5 for a start. This will also require some testing out to get it right.