Most of these things can be fixed by editing (using MS Notepad) the aircraft.cfg found in the aircraft's main folder. You ought to back it up before making any changes.
1) Hovering over the runway - if the aircraft appears too high off the ground, adjust the figures in the [contact points] section. Points 0,1,2 correspond to the gear, the remainder are "scrape points" around the airframe:
[contact_points]
point.0= 1.000, 13.75, 0.000, -6.590, 8662.205, 1.000, 1.000, 35.000, 0.800, 2.000, 0.09825, 2.000, 2.000, 0.000, 260.000, 260.000
point.1= 1.000, -8.60, -6.250, -6.805, 8662.205, 1.000, 1.250, 0.000, 0.750, 2.500, 0.9775, 2.000, 2.000, 2.000, 260.000, 260.000
point.2= 1.000, -8.60, 6.250, -6.805, 8662.205, 2.000, 1.250, 0.000, 0.750, 2.500, 0.9775, 2.000, 2.000, 3.000, 260.000, 260.000
point.3= 2.000, -9.083, -19.500, -0.167, 1574.803, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 5.000, 0.000, 0.000
point.4 = -0.88, -7.19, -6.42, 1500, 0, 0.5, 22.0, 0.3, 2.5, 0.7, 4.0, 4.0, 0
point.5 = -0.84, 7.17, -6.43, 1500, 0, 0.5, 22.0, 0.3, 2.5, 0.7, 4.0, 4.0, 0
static_pitch= -0.067
static_cg_height= 6.000
gear_system_type=0
You will have to experiment by changing the values and testing them out. This will also correct the dirt/spray occurring too far from the wheels.
As for the lights, positioning the strobes & navs are a similar process, this time you go to the [lights] section,. Adjusting these values changes their location. In the example below, light.0 is positioned -16.03 feet back from the CofG; is to port, -23.19 feet; and, is 1.79 feet above the CofG - note that the starboard light is positioned at 23.19 feet, the same distance but in the the opposite direction.
[LIGHTS]
//Types: 1=beacon, 2=strobe, 3=navigation, 4=cockpit, 5=landing
light.0 = 3, -16.03, -23.19, 1.79, fx_navred
light.1 = 3, -16.03, 23.19, 1.79, fx_navgre
light.2 = 1, -17.01, -22.93, 1.82, fx_strobe
light.3 = 1, -17.01, 22.93, 1.82, fx_strobe
light.4 = 1, -7.50, 0.00, 2.55, fx_beaconb
light.5 = 1, -0.75, 0.00, 6.25, fx_beaconb
light.6 = 1, -25.81, -9.36, 9.92, fx_beacon
light.7 = 3, -25.81, 9.36, 9.92, fx_navwhi
light.8 = 3, 15.27, 0.00, 6.38, fx_vclightwhi
Lastly, for landing lights illuminating the ground, this is due to FSX having different coding for landing & taxi lighting, and can only be added in the model when compiling it. You would therefore require the model's source file to modify it. In fact, not all design programs even permit adding fully functional landing lights in FSX, as I have found out with FSDS3 - a great program to work with, but unfortunately suffering this shortcoming. So, you can fix much of this, but not everything.