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