X2 is also closed for a refurb. When I rode Viper I did see a train outside of the station, not sure if the other one was in the station, but there was some activity going on.
Most operations will shut down their rides when lightning is in the immediate vicinity. As far as rain, it depends upon how safely the individual rides can operate under wet conditions since speed and braking are effected.
Bring a Poncho, rain jacket, umbrella or all the aboveI highly suggest you have all of these when you are visiting any park in the rain. If you only have access to a rain jacket no worries! Six Flags America sells ponchos and umbrellas for the whole family.
Go EarlyIf you want to avoid long lines there's no simpler way than to wake up early and get to the park before it opens. Whether you have access to early entry or not, being at the park entrance before it opens will save you lots of time. Usually, you can get in 2-3 rides during the first hour of park operation.
Weekdays in April, May, September, October, November, and December are typically the least busy days. Always research for special events that may be going on that can cause abnormally large crowds (the park is reliably busy during spring break).
Everything is more spread out, so you'd be caught longer in the rain. Based on the usual summer forecast, we'd recommend a plan that includes visiting Animal Kingdom in the morning and EPCOT in the afternoon. Magic Kingdom and Disney's Hollywood Studios each have a fair amount of indoor attractions.
Epcot is the best because there is only one outdoor attraction in the whole park, Test Track. Other than that, every ride will remain open and running during rainy weather.
Disneyland in the Rain Park OperationsThere are a few attractions that will close during rain, but many remain open and Genie+ still works in the rain too. Remember safety is the most important factor and some rides may open and close depending on the severity of the weather.