First time is always the worst. Looks like minor sprag spring damage on gear, ensure theres a new one in there and all the old bits out before closing up, magnet fishing. Pretty sure installing tomos side cover has been gone thru a zillion times on MA but here goes;
There is no magic, the side cover just goes right on, no real force needed, maybe a just a couple wiggles, and a couple small bumps with your closed fist and bam. Things to look out for:
1. Ensure peanut in fully in slot
2. Ensure pedal shaft is all the way in, wiggle wiggle, twist twist, until it seats all the way in...this is your issue i believe
3. Ensure washers are all there for spacing.
4. Ensure no crap in alignment slugs n holes.
5. Ensure you have a new case gasket.
6. Ensure above and install cover straight, keep some inward pressure on that pedal shaft so it does not twist and pop out. Take side cover and wiggle wiggle, to align counter shaft and up slightly for crank shaft. Once crankshaft is on and alignment pins located then it should be close 1/4" or so. Make sure that pedal shaft doesn't slide out, push push, wiggle wiggle, tap tap, If it 1/8th or so from flush, you've almost made it, a couple fist bumps and your set. Whatever you do, do not use screws to "pull" that last bit of cover on.