The image being too dark with your PAL SNES cable means the N64RGB board is set to NTSC output. If your modder closes the J1-J3 jumpers then you can just use your PAL SNES luma sync cable.
If the J1-J3 jumpers will be kept open then a Gamecube cable with composite video as sync will work but you will get diagonal lines in your image if you don’t order the shielded packapunch cable. Another option is to ask the seller to change the regular Gamecube cable to luma sync. This is all with the assumption that composite video and luma on your N64 were not changed to composite sync by your modder since we don’t know that yet.
3. You have to decrease V.backporch to 15 if you increase V.active to 288.
IMO your modder should fix the color issue free of charge. It seems that he didn’t check the N64 before sending it back?