Ok, so here are my resources and where I'm at right now. It doesn't seem to be a consistent problem, apparently CPU Usage and Memory Usage is spiking sometimes, which triggers the warnings. I am running 7 Wordpress sites on that, with a combined 4,200 hits per month (that's what the GoDaddy rep said). Which seems like very little. I talked to GoDaddy, the dude had me click on some PHP optimization options and compression, but said Wordpress has become very resource intensive and I should consider upgrading (that sounded like a sales pitch for the sake of it). I will now check out the Sucuri Scanner plugin, thank you!
Here are the stats for the 7 sites: http://imgur.com/a/FmSPp Mhmmm, according to those stats I guess the 4,200 hits were daily. Edit: Ok, I just realized I'm getting a ton of referral spam... can that be an issue? Now on to blocking it.