Are the 1k resistors on the base needed or should they be a different value?
The transistors in your circuit are emitter-followers with a very low base current so the 1k resistors can be replaced with wires.
Are the 1k resistors on pins 3,5,10 and 12 needed or of a different value?
They can be up to 33k ohms but each pin needs an additional resistor to ground as an attenuator so that the input voltage never goes higher than the supply voltage minus 1.5V.
I reversed the vcc/2a and /2b resistors because on the turn signal portion I didn't want output until a higher voltage. Would higher value resistors be better?
You don't need opamps nor transistors for the turn signals. When the turn signal voltage is 13.8V then it can turn on the LED for that side.
Should I or do I need to add some pull down resistors to pins 3,5?
You don't need 4 opamps since only two opamps from an LM358 dual opamp are needed for the brake LEDs.
Since these are extra lights on the side bags. When I remove the bags the leds will no longer be in the circuit. Do I need to add anything to the circuit for when the leds are removed?
A weatherproof jack.