Right, Im at my wits end with this one now

I have an old 98 1.8 zetec with 116k on the clock as a daily run about, recently it started over revving and pulling on its own so I checked and replaced the usual suspects,crank/vacuum hoses and throttle cable. I have also replaced the TPS and cleaned the MAF.I have replaced the clutch and brake switches on the peddle assembly too.
All of the above have sorted the over revving issue but now the revs hang in between gear changes but only changes above 3k revs. Changing gear below this the revs drop fine, Im thinking it may be something to do with the VSS but rather than change that I thought I would ask.
I know there was a problem with early inlet manifolds but the car has run perfectly for the two years ive owned it.

Im starting to get annoyed at the lethargic gear changes waiting for the revs to drop so as to not burn out my clutch

 

Now all sorted, I had failed to seat the induction hose correctly on the throttle body thus allowing a small amount of air to bypass the MAF