Sputtering during acceleration?
 

I have a 92 4runner, 4 cylinder, 5 speed standard, 4x4. A while back my truck started sputtering under acceleration. I changed the fuel filter and that seemed to solve the problem for a while, and I figured I must have some gunk in my gas tank (as I have replaced it with a used one) and I don't really let my tank get under 1/2 tank and never below 1/4 tank, to avoid this happening again. However months down the road I have a sputter again.... I don't feel it's the same thing again (could be wrong) and I'm at a loss of where to go next.
I already replaced the distributor cap and rotor and I recently did an oil change. After the oil change it stopped for a while and I thought that must be the problem as it stopped immediately after I did this, but yesterday it started again. It does it in 2nd gear at around 3500RPM and 3rd,4th and 5th once you get to about 28-2900RPM. I've never had it do it at an idol.
Could it be my fuel filter again?! even though I haven't let my tank get low?
I've had a buddy (who is a mechanic) look at the spark plug wires and he thinks they look fine, granted we haven't tried new ones. And I've been thinking about replacing the spark plugs anyway, see if that helps.
Any other suggestions?
Also it wouldn't be the fuel pump would it, it wouldn't start and stop going again?
Oh and one final thing the clutch has been slowly going for quite some time started slipping a bit about 3 -4 months ago, rarely does but does need replacing eventually, could that have any effect on all of this?
Any help would be great I'm a bit lost...