Are the 88 and 89 si harnesses interchangeable? Having a hard time finding an 88

 

they are not exactly the same - the 88 has a rectangular 6-pin connector at the driver's side firewall connection - the 89 has a round 8-pin connector at that location - you could swap a different connector onto either the engine harness or the chassis harness and make it work

 

How much of a pain is it to switch

 

It's not just the driver side plug that is different. The passenger side plugs are completely wired differently.