[8bit]

Gas mileage is important, especially with the variable gas prices. I was just reading about the 1977 Firebird Formula 4 speed with the then new economy 301 ci V8. They recorded 21 mpg combined city/highway, which was good for those days.
Your fuel filter is part of the induction set up? Often it's located next to the electric fuel pump towards the back of the car. Anyway you can try some of those fuel system cleaners, there are various brands. I haven't used any for quite some time but some people think they are good. I am tempted to say that you might have had a particular bad tank of gas, but, that happens less often these days than it used to.
From what you said did you add a performance chip to the car? If so that might be producing the rough idle and loss of performance initially and into third. Sometmes these chips boost engine power by sacrificing some torque, so the engine feels stronger when you go for high revs, but lower down in the rev range (lower down the power curve) it can make the engine feel a bit sluggish. This could explain why you feel that loss when shifting into third, by going into the taller gear after 2nd the revs drop back and you get back into that sleepy part of the rev range. Also by creating more top end power the chip could have introduced additional idle roughness compared to a stock standard chip. Designing a good performance chip isn't easy.
Could you swap the normal chip back into the car and see if the problem goes away? Alternatively, if the car is still using a standard chip, try another standard chip. It's possible there might be something wrong with the current one in your car. They make so many of these chips that a certian % are faulty.