Grinding noise when starting

When I start my truck, it makes a grinding noise; like something is turning and grinding. It does this in park while idling and also when being driven. I want to say a couple of times it seems like the engine bogged down to some degree as if something was causing friction on the motor. I thought it might cease but it didn't. It doesn't do this every time I start it but it has a few times. Truck doesn't seem to be running too bad aside from this. No overheating or anything but want to say maybe a little loss of power and just a wee bit of a rough shift which it wasn't doing before. I bought the truck about 2 years ago. It sat for about a year and a half. I did start it several times though, I haven't really been driving it just an occasional trip to the store a couple blocks away. I'm thinking maybe the trans fluid and filter need to be replaced. I was going to start there. Oh, and I do have a bad water pump which leaks water from the gasket which I am in the process of replacing. Don't know if a bad water pump would make the grinding noise and tax the engine. I doubt it. But any advice, ideas, or instruction would be very much appreciated. Thanks fellas