There is a service bulletin out on that code. It says that if a p1298 is stored, then the electrical load detector (ELD) may have a faulty solder joint. If you just did a motor swap, I would check all the connections at the fusebox. You used to have to replace the under-hood fusebox to fix it, but replacement ELDs are now available. The P/N for the Civic one is 38255-S5A-003.

Hope that helps.