Your shop is guessing, a clogged fuel filter would cause engine speed to slow down. You said your engine is speeding up ("when I hit around 40 MPH the RPM's will raise to 4 or5 and my truck has a hard time gaining any speed.")
Do you have a manual transmission? What gear are you in when this happens? Is it more frequent when going up-hill? If yes to questions 1 & 3 and you are in 4th or 5th gear your clutch is probably slipping. A slipping clutch may be corrected by adjustment but it's usually caused by a worn clutch a new clutch is needed.