It could help, since you're starting over with a completely dry intercooler that won't have any condensation/blow-by buildup. However, the "EcoBoost Shudder" is a multi-faceted issue that doesn't necessarily have a single cause. To cure the issue as best as possible, you should try cleaning out your factory intercooler, changing your spark plugs to iridiums and regapping them to .028" to .030" if you're running a tune, or .030" to .032" if your truck is stock. Adding a catch can is also beneficial, and can help prevent blow-by buildup. Replacing the factory intercooler can help, but should probably be your last step, given the costs involved.