In short, I would not book that train/plane combination as you have proposed based on your circumstances.

If you do decide to do this then you should absolutely do online check-in the night before. The cut-off is 60 minutes prior to departure to be checked in and to have your bags dropped off at the counter. See this thread if you want to understand what can happen if you don't meet those times.

If you are checking bags there is no way I'd chance it.

If you have never flown CO internationally before such that your passport isn't scanned into the system - a scenario that will prevent you from doing online check-in - I wouldn't chance it. And you noted that you'll probably fall in to this category.

Any chance that the PHL-IAH-CZM routing all on airplanes is competitive in price? You'd probably be on that 5:35am out of PHL but you wouldn't have to bother with the train or EWR.