Some more news!!
First, I tried to socket the WRAM and have the same results.
Even with 3 different SRAM chips

Them, I tried to build another clock generator and substitute the actual one.
I ended like this:
Attachment:
File comment: New Clock Gen
4550c658-0449-4e34-a458-6bad5736c555.jpg [ 180 KiB | Viewed 968 times ]
At first it seemed to be the deal, I was playing Crisis Force and everything was smooth.
Them the game froze for about a second, but continued. Weird!!
But when I arrived at the part near the 1st boss where the floor opens, it crashed!
I tried Megaman 2, and got he same Crashman's crash. Gradius was the same thing too.
So, with no other ideas, I just tried an original NES CPU I have from that flooded NES.
Intestingly, the games worked flawslessly!! Only Gradius is still giving me trouble.
By the logic, the problem would be on the clone's CPU.
I tested it on the other clone and again, it worked flawlessly! This time even Gradius worked fine.
Taking a better look at Gradius' board, after supposing it was some kind of protection related to the diodes that some of original famicom boards use without success, I noticed the the 74'161 pin 3 is with a steady voltage of 0.8V on the Phantom System, while in the other clone the same pin gets a voltage of around 4,5 volts.
I think this means that D0 is getting pulled to the logical level 0 on the Phantom System, while in the other clone it's floating, as it should in normal operation.
I tried some pullups on this pin and all that I could get was a non working game, that was cured as soon as I removed the resistor.
Could this possibly be ralated to a bus conflict?
Interstingly, there's an empty space on the board wich ressembles a 14pin IC and is like this:
Code:
O O--Vcc
|
/ROMSEL--O O
O O
|
O O
CPU R/W--O O
PRG /CE--O O
GND------O O
The PRG /CE pin comes from the PRG epoxy ROM and is bridged to /ROMSEL. The other pins (including /ROMSEL) come from the cartrige edge connector.
I just could not imagine what IC should be put in there to possibly avoid bus conflicts, any suggestions?
Looks like I should try to cut the PRG ROM's /OE and add an inverter to R/W on it. Could this possibly solve the problem?
I just don't understand why this happens with an clone and not with another.

I thing this is really weird!! How come this stuff have trouble just like this!!?
I really hope that someone that is reading this can help me to throw some light on it, at least the Gradius problem...
Anyway, the problems are almost all solved! And I sincerelly hope that this discussion can be useful to someone else in the future.
Sorry for this big wall of text...
Thanks in advance.
Edit:
Pictures of the Gradius' PCB.
Unfortunatelly it's not mine, but it's the same model.
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Gradius cce - Componentes.png [ 1.09 MiB | Viewed 957 times ]
Attachment:
Gradius cce - Solda.png [ 1.27 MiB | Viewed 957 times ]
Mine is without the transistors and resistors, I added 2 diodes and is a lot more wornout.