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Did you check for misfires? can you scan for trouble codes? what did the filter and fuel look like when the pump was changed?
You might have some injectors getting clogged. I would try disconnecting the injectors on the vehicle while it is running and see if the rpm changes. It should drop each time an injector is disconnected. If the rpm does not drop when pulling the connector the injector is failing or clogged. You can also check the EGR for leaking or for sticking open from carbon. If EGR is leaking it will cause a vacuum leak and a rough idle.
let me know what you find