These are some thoughts on how to minimize the cost of the VI.

PCB Design DFM

Increase spacing between pin-through-holes(PIH) and surface-mount components(SMT) to allow wave soldering. For next iteration, potentially separate the two as much as possible.
Negatives: none

Remove Bluetooth

Cost Savings: ~$25 (1000 unit quantity) by removing the module, associated components on board and the slight size decrease that would be possible.

Negatives: No wireless support, USB only.

Use a different MCU in the same family

Cost Savings: ~$2 (1000 unit quantity) by going with the LPC1754 (half the price of the LPC1769)

Negatives: Only 1 CAN controller

Use a different MCU from another family

Cost Savings: ?

NXP's Cortex-0 family doesn't have CAN controllers. The PIC32 family is generally more expensive than the LPC1769. Any other options?

Remove 12v power port

Remove 1 RGB LED

Cost savings: $1

Remove 1 button

Cost savings: ~$0.35