Boy, rough idle seems to be a pattern...
My issue seems to be when running up through the gears (5 speed) the engine is rough and hesitates as well as rough idle...
Just changed the fuel filter, but the rough idle is still there. I fear the test drive will prove no change....

Fuel filter had no change. It runs rough accelerating through third gear and above.

Ideas?

 

Rough means misfires
Clean the MAF sensor, needs to be done once a year, its easy to do
Run a can of Seafoam, or similar injector cleaner, in the gas tank once a year

I would pull out the spark plugs and have a look at each tip to see if any cylinder looks like it is running rich or oil fouled

I would also do a compression test on each cylinder while spark plugs are out, just to take that issue off the table so you don't waste time and money on non-fixes if it is a compression issue

If spark plug wires and coil pack are original then I would replace them just as general maintenance
Spark plugs are a judgement call after looking at them, clean and re-gap if they look OK

O2 sensors are the only sensors that "wear out", they last 100k miles or 12 years, then need to be changed, they pay for themselves a few times over, in the next 100k miles or 12 years in best MPG fuel savings