Hi Austin & welcome to Ninjette!
Can you take photo of "rod things" and post here? Also of fairing pieces that should go onto tank brackets.
Order of operations is critically important here in getting everything to line up. Also never ever tighten bolts all way down until you get every single panel in place. The taillight alignment actually depends upon front-fairing being in correct place.
This is for '08-12 new-gen models:
1. install fairing-stay onto frame. Note that two big bolts allow some wiggle, so leave loose as this will allow about 1/4" of movement back at gas-tank bracket.
2. install headlights into fairing (leave windshield off). These bolts you can tighten because nothing else attaches to headlights
3. install inner mirror bracket onto fairing-stay
4. lay fairing over mirror bracket and lightly thread one mirror bolt from outside to in to hold in place
5. install instrument cluster into inner fairing
6. install inner fairing over fairing-stay, lining up upper bolts behind mirror bracket
7. install inside mirror bolt through both fairings and bracket (loosely)
8. align inner and upper fairing over tank-bracket and lightly install bolts
9. align side of upper fairing with lower fairing-stay and lightly install bolts
10. install windshield. Lower bolts actually go through windshield and through upper fairing and into well-nuts on inner-fairing. Three layers needs to line up perfectly