If this subject makes no sense to you just move on.  You won't understand the rest of the question.

After a long hiatus I fired up Bonzoni's B-52 and noticed the nav/strobe/beacon lights were way out of whack - about 20 feet behind the aircraft.

I downloaded the original aircraft again and I saw that aircraft.cfg has no [Lights] section in it all, so I don't know where mine came from.

Anyway, mine reads:

[LIGHTS]
//Types: 1=beacon, 2=strobe, 3=navigation, 4=cockpit, 5=landing   
light.0 = 3, -133.50, -93.00,   -1.65, fx_navredh ,
light.1 = 3, -133.50,  93.00,   -1.65, fx_navgreh ,
light.2 = 3, -190.10,    0.00,   4.4, fx_navwhih ,
light.3 = 2, -133.50, -93.00,   -1.65, fx_strobeh ,
light.4 = 2, -133.50,  93.00,   -1.65, fx_strobeh ,
light.5 = 2, -178.00,    0.00,  29.70, fx_strobeh ,
light.6 = 1,  -85.05,    0.00,  7.15, fx_beaconh ,
light.7 = 1,  -120.22,    0.00, -7.50, fx_beaconb ,

Does anyone have an aircraft.cfg that puts them in the right place so I don't have to reinvent the wheel?

I could be wrong but I think that Bonzie created that B-52 in FSDS1. In that case the lights are defined in the MDL file. You can add the FS2002-style lights in Aircraft.cfg but I don't think it's possible to lose or move the originals, meaning you will end up with 2 sets of lights.