904 Trani
As Michael said there's different versions of 904's. Nearly all slant 6 904's came with the amount of frictions and steels you said yours has. Even 318 904's sometimes didn't have any more than that. Only the heavier duty 998 and 999 (versions of the 904) have 4-5 frictions in the clutch packs. I wouldn't cut .125 off the pressure plate. That'd make it nearly as thin as a steel plate cause their only about .215 thick from the factory. IMO it'd likely bend and fail if you cut it that much. You set the clutch pack clearance via selective snap rings. That's the snap ring that holds the clutch packs together and they come in different thicknesses. By your description of the clearance issues your seeing I wonder if you have the rear clutch and front clutch friction discs mixed up. The friction discs for the rear clutch are a lot thinner than the ones in the front clutch pack. The discs for the front clutch pack measure about .086" thick while the ones in the rear pack measure about .061" thick.
A manual valve body is common to see in a high performance application. Nearly every racer that's running a 904 uses one. Make sure you get a valve body with low gear braking. Without low gear braking you can trash the sprague if your not careful. Leave the "no low gear braking" valve body's for the racers
What manual do you have that claims all 904's have that many clutch plates per carrier? If it has that error I'm not sure I'd trust it for anything else it says.
In addition, I wouldn't worry so much about your slant 6 tearing up a 904. Racers have been using 904's behind very high powered V8's for yrs. If they'll last behind that your slanty isn't going to trash one very easy. Not putting down the slant, it's a great engine but it doesn't produce enough torque to scrap a 904 too easily. That's why slant 904's only have 3 clutch discs per carrier. I'd be more worried about that puny 7-1/4 rearend grenading.