I have made some edits to the above list taking into consideration the above input from others. Also I removed the low profile heads as there looks to be plenty of clearance. Also added was Flywheel cover bolts. McMaster numbers are included but it would cost $37 to order from there as you would receive a total of 170 bolts since they are all sold in packs of 10 or 50.
All have a drive size of 5mm, this is the largest for maximum strength.
2x 35mm Black Oxide M6 x 1mm (97050A229) : Internal Case Bolts
4x 35mm Zinc Plated M6 x 1mm (90128A267) : Flywheel Cover Bolts
4x 40mm Black Oxide M6 x 1mm (91290A203) : Internal Case Bolts
6x 40mm Zinc Plated M6 x 1mm (90128A268) : Clutch Cover Case Bolts
4x 50mm Zinc Plated M6 x 1mm (90128A269) : External Case Bolts