Cutting lines from well to pump

tibberous

Here is a picture of my pump:


There are two black pipes that bring water in the house - they are joined together right when they enter the wall.

What I want to do is shorten the lines so I can move the pump into the corner. Then I want to take out at least one section of hose and extend copper lines that are already there closer to the pump, and add in a big blue water filter.

Pretty confident with the first part, since I had the water filter hooked up right before I took the photo's (thus the buckets) One of the hoses is dripping out of the part before the threads - not sure if it can be fixed.

Part that has me worried is cutting the water-in lines. I'm thinking if I cut the pipes about a foot out of the wall, I can add a 90 fitting and run it straight down the wall.

On a side note - whenever I shut the water off and then turn it back on, it's solid rust for a couple minutes. Is there any way I can flush out rust short of turning everything off and back on? My new sediment filter is already brown =/