Listed below are Things I can tell are different between the two nintendos
The biggest differences I found are the use of 74LSXXX and 74HCXXX ICs
And the missing 4Mhz CIC. Not really sure what the part is called? Ceramic Resonator?
I am leaning toward the 74XXXXX ICs.

The NES that does not work with the powerpak when rgb modded.
nes-cpu-04
SN# N1394910
Different part numbers
U3 HD74LS139P
U2 HD74LS373P
this system is also missing a few components.
C11 .01u Ceramic Cap (near the blue power connector)
C12 .01u Ceramic Cap (near the blue power connector)
4Mhz Out CIC (circuitry/lockout chip clock line). runs to pin 71 on the cart. It has 2 empty holes. (near the 3193a lockout chip)
Any other newer nes-cpu-07 Nintendos I looked at have a 3pin(one pin to gnd) light blue 4Mhz cic on them.
---------------------------------------------------------------------------------------

The NES that does work with the powerpak when rgb modded.
nes-cpu-04
SN# N1284385
Different part numbers
U3 TC74HC139P
U2 TC74HC373P
This nes 4Mhz looks like a Ceramic Resonator. It is red/orange in color.
I would guess it uses 2 pins. I mailed the nintendo back and can not verify that any more.
but the v4 nes I have now only has 2 holes on the pc
-------------------------------------------------------------------------------------
There is a difference between the power/RF/AV daughter board.
There are only 5 pins going to that. 2 for power, 1 gnd, 1 composite video and 1 mono audio.
I have a hard time believing that will effect the ppu or the powerpaks graphic abilities.
Both nintendos have 74LSXXX silk screened on the pcb by U2 and U3.
The working nes uses 74HCXXX ICs even though the silk screen calls for the the other 74LSXXX.
while looking for info on 74 ICs I found this on a site.
The 74LS (Low-power Schottky) family (like the original) uses TTL (Transistor-Transistor Logic) circuitry which is fast but requires more power than later families. The 74 series is often still called the 'TTL series' even though the latest ICs do not use TTL!
The 74HC family has High-speed CMOS circuitry, combining the speed of TTL with the very low power consumption of the 4000 series. They are CMOS ICs with the same pin arrangements as the older 74LS family. Note that 74HC inputs cannot be reliably driven by 74LS outputs because the voltage ranges used for logic 0 are not quite compatible, use 74HCT instead.
It sounds like the all nintendos really should only use 74LSXXX ICs. But I have saw one with 74LSXXX ICs.
Does any one have any feed back on this. Expecially the 4Mhz part and 74XXXXX ICs.