Welcome to the PF. And very nice quality work so far!
Designing an Engine Control Computer (ECC) and hardening it against electrical transients and RF interference is very non-trivial. Is your motorcycle intended to be licensed and ridden on public roads? Or will it be more of a show vehicle?
The area of Electromagnetic Compatibility (EMC) is quite large, and involves a lot of design and fabrication techniques. Here is a Google search with typical web pages with EMC info:
But to really do a good job at hardening your ECC and the bike's electrical system, that may need you to partner with somebody who has a lot of experience in this area.
And beyond the EMC hardening aspects, there is also the issue of processor execution reliability and rider safety. The system needs to have some "fail safe" aspects built into it, and it would be best if there were redundancy of critical processing components like the PIC. One design technique would have 3 PICs all running the same program simultaneously, and "voting" on the outcome of that processing via an external control circuit. I'm not sure if commercial ECCs use multiple processor redundancy to increase reliability, though. In things like plane flight computers and such, I think it is relatively common.
Others will hopefully chime in with thoughts as well. But a lot hinges on whether you want to license this for public road riding, I think.