If you have the pump off, you can get a clothes hanger and open it up all the way. Bend about a 1/2 or 3/4 inch hook in the end and force it through to the last cylinder and start jamming it in and out. It will take a while, but you'll loosen things in there. Also remove the block drain and work your coat hanger up until you get some water flowing through there. Then replace the block drain, get a bottle of CLR or two and pour them in until the CLR is right up to your pump opening (remember your block slopes backward a lot). Now leave it alone for a few days, drain and flush. Repeat if needed.
Alternatively buy a pound or two of powdered citric acid and make a very strong mixture of it and tap water and pour that in there. Either will dissolve rust.
And for a third alternative, buy a gallon of 45% vinegar and pour that in there...but don't leave it for a couple of days. 45% acetic acid is vicious stuff. You just want it do to the work and then get it out. 8 hours might be plenty.
And if you bought that citric acid, you can make a really good cleaner to use in your house. Mix two tablespoons into a quart spray bottle to get about 6% solution. You can clean toilets, lavatories, bathtubs and especially stainless steel sinks like a wizard with this...BUT NOT GRANITE, COLORED GROUT OR STONEWORK. You'll just ruin those things if you use it for them.
Good luck.
