Here is info from Dana Bell on P-51 wheel wells.
Anticorrosive colors and P-51s...
Tue Aug 27 10:19:29 2002
There are really three phases of wartime painting of Mustang wheel wells - all related to corrosion control. At first, the metal surfaces were to be painted with one coat of zinc chromate (yellow), one coat of tinted zinc chromate (green), and one coat of aluminized lacquer. This finish appears to have been limited to Allison-engined Mustangs.
Two things happened in 1942. First, a shortage of aluminum ended the use of the aluminized lacquer and forced the reformulation of green zinc chromate. (This led to the use of other colors for wheel wells and struts - for example the Neutral Gray on Lightings and Bronze Green on some P-39s and B-29s.) Second, the AAF allowed North American to produce AT-6s, B-25s, and P-51s without primers to ease production. (Boeing got similar permission for its B-17s.) This is what led to the unpainted wheel well noted below. Throughout this period, the wing spar appears to have consistantly carried zinc chromate (yellow) primer. (The primer reduced corrosion where the spar contacted the aluminum sheet and reduced the buildup of static electricity - an important issue with the fuel tanks mounted just aft of the spar.) This combination, as noted below, was common on Bs and Cs, and most Ds and Ks.
By 1944, the AAF was receiving complaints about corrosion in a number of aircraft, including the Mustang. Some unspecified action was required, particularly to reduce dissimilar metal corrosion between structural members and skin panels. Some manufacturers gave the structure a coat of yellow zinc chromate before adding the skin. Some left the structure unprimed and gave the inner surface of the skin a coat of yellow zinc chromate. It's not clear how North American handled the problem, but there is one undated color shot of a P-51D (or K) production line showing the entire wheel well primed in yellow.
This is just a general explanation - it won't help you know what color the wheel wells would be on any particular aircraft. But you can make your own informed decisions based on the date you suspect any particular aircraft (and not just a Mustang) was manufactured.
Here's a wartime color pic of a P-51D with silver wheel wells.