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I don't know if this has anything to do with this, but when I picked up the car, it had virtually no petrol in it. It was limping and slowing the engine down, so I pulled over so we could get fuel in a can, put that in then get to a garage. After I put a full tank in it's driven fine for the last two days.
However, I was driving it home tonight and and it was slowing down at 3000 rpm and i couldnt speeed up or accelerate up hills. I got home and it sorted itself out.
I'm wondering whether some of the gunge at the bottom of the tank is still making its way out? Or does anyone have any other ideas or experience on this?

One thing that springs to mind with an engine that will only rev up to 3000RPM is, either it has gone into a "limp home" mode, or the car road speed is not being recognised correctly by the engine's ECU - so the engine ECU thinks that the car is stationary, so limiting the revs to 3000.

As you have not said that any instrument panel warning lights were lit at this time, it just might be the second of my suggestions as the car might not have been able to work out that there was an actual problem.

Though as you said, it might be some gunge moving around, if it partially blocked the fuel outlet in the tank it could cause fuel starvation that might just recover at next engine start, if it had drawn the gunge up into the fuel filter, that starvation would still be exist.