You need to cover the alternator, and an exposed CAI filter if you have one. It would also be a good idea to cover the ECM/ Fuse box. Try to avoid soaking the wiring harness. Mainly because over time, the water can migrate down the wires to the connections, leading to corrosion.
As for the coil packs, I would cover them entirely. The reason is twofold. First, the coil packs themselves don't seem to like getting water in them. This is an issue with the F-150's and may be due to the potting material aging and allowing water into the coil. The second reason is the location of the plugs. Unlike older cars where the plug was exposed, these plugs sit deep in the engine. If water gets around the plug it has nowhere to go until it eventually dries out. This water can also wick up into the boot of the coil pack, which may be another reason for coil pack failure after a good soak. Looking at pictures of the '01 in books I have, I can't tell how deep your plugs sit. Admittedly, this is anecdotal information based on a similar engine configuration. All I can say is I wouldn't risk it.
An occasional rinse should not damage the connectors. These engines are, after all, designed to take some weather and abuse.
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2001 gt. what exactly do I cover under the hood while cleaning?? 
