You're fine milling the tcover which will move everything(fan assy) rearward & the alt can be easily spaced rearward to keep the pulley alignment correct but see where you are at with the crank pulley. Mock everything up before you cut and you ideally want ~.040" between the vanes and the tcover flat(including gasket) and on the water pump you can press the vanes closer(forward) to the pump body body(support the front shaft when you do so)(which makes the WP even more efficient)and which allows you to mill the tcover more to give you even more fan to rad clearance DEPENDING if your pulleys can be spaced into alignment. also the face of the harmonic dampener can be milled so the crank pulley will sit further rearward. that'd be extreme & I did not have to do that myself but I wanted to cover everything for you.