you can just block off the coolant line that runs to the throttle body, ford used to to just give a "consistant" temp at the throttle body, which on some days, its nice, and other days, it robs you of a little bit of power
as for deleting all the rubber hoses, you have to remember that 86 is the first year for the 5.0 with full EFI, and Ford didnt have it very well refined, so over the years, things changed. The cobra intake you have is modeled after the 93, where as your stock one is the first year, so there will be some differences