Does anyone know of where I can get code to do protein structural alignments in perl?

Welcome to the Monastery first of all. Getting code isn't the goal, since you want to make judgments on whether it fits your requirements according to the type of alignment tasks that you want to perform, that might require you to customize it and maybe break your head over ambiguities in there since you might get to deal with OpenGL and 3-D rendering issues among other things like calculating RMS or figuring torsion angles, structural alignment is a different concept than sequence string alignment and it requires more skills...

Since you want to do structural alignments anyways, have you considered the free DeepView since it is an established Structural Alignment Tool and it has a very nice step-wise accompanying tutorial too, so maybe investing time in learning it provides a higher trade-off ...