A defective vacuum line can cause a whistling sound when the vehicle is accelerating. A loose belt can also create a high pitched whistle sound.
look to see if your intake manifold is gummed up with residue
You have no wheels. - Geoff
A vacuum leak usually from the intake manifold gasket or brake booster hose/connection will cause a whistle upon partial acceleration. It will usually go away when your foot is off the gas or when more throttle is applied.
Many time the high pitched whistle will be cause by a loose or unattached vaccuum line on the engine.
The most likely cause is a dirty fuel filter that starves the engine.
will the transmission causes my 1999 ford expedition to bog down & sputter when accelerating the 4.6liter engine.
most likely an intake gasket
A damaged catalytic converter could cause that.
Gasoline pedal/air intake pedal
an air leak in your intake will cause the engine to rattle. Protege's intake hoses are prone to cracking.
Check to see if any of the air intake pipes/tubes have come off or are loose.
Depending on the extent of the clog, it could cause the engine to lose power under a load or accelerating and in severe cases the engine may not run above an idle. I don't see it causing any one cylinder to missfire.