Yeah, routing the wire harness through the lower intake definetly was not the smartest move for us having to do maintenance with our 80's but I guess that it made sense to Toyota at the time with the assembly line process for on reason or another.
When I pull my harness out I can look and see how feasible it would be to adjust the hard plastic and tape around the wires so that it comes up just aft of the intake plenum instead of through it.
I'm playing the devil's advocate here (cuz its fun ), but the intake manifold isn't a "serviceable part" designed to be removed as part of regular maintenance. There is no need for Toyota to make it an easy-in, easy-out part, nor is there a reason for them to do so. The clamshell shape of the intake manifold is also a great design in that it protects fragile/expensive/critical/low maintenance parts (wire harness/sensors/injectors/fuel lines/VSVs etc) from clumsy handed grease monkeys such as ourselves .
Next you'll start complaining that the pistons are too hard to get at!