Wasn't sure where to post this so I'm putting it here. I played through the game trying to collect all gems to get a count on the gem total in the game. Here's my list:

NOTE MY LIST IS NOT CORRECT.

Total: S388 E380 R380 D383

Pre Level: Beach: S25 E18 R17 D12 Ring of Fire: S25 E18 R17 D15 Town: S18 E19 R19 D19 Flower Pods: S25 E17 R18 D16 Tesla Trees: S18 E18 R19 D19 Frozen Islands: S25 E13 R18 D15 Main Valley: S18 E24 R16 D14 Drill Area: S18 E25 R16 D16 Spotlight Area: S17 E24 R17 D16 Volcano Area: S18 E17 R20 D19 Battle Platform: S19 E17 R20 D19 Conveyor Belts: S17 E27 R16 D17 Fire Caverns: S19 E17 R20 D20 Guardian's Fortress: S18 E18 R18 D19 Water Slides: S19 E15 R18 D21 Air Tubes: S15 E15 R20 D25 Great Tree: S15 E15 R20 D25 Atmospheric Projector: S15 E15 R20 D25 Life Realm: S18 E19 R19 D19 Death Realm: S29 E30 R29 D28

That brings me to the total MachineDJP got in his walkthrough of the game. His total was: S386 E383 R381 D386

That means I missed some gems he got but I also came out with 2 more Sapphires than him. So I don't think we can one hundred percent confirm the total of gems in the game for the 100% category.