Awkward pulsating idle

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2002 Mazda Protege 5
I recently purchased a 2002 protege5 and it has been good so far, other than the water leaks, my question is, when the car is at idle, it idles fine in neutral, does not matter I clutch pedal is in or not, but as soon as the selector is placed into any of the gears (manual transmission) the Rpms will increase, and sometimes jump up and down by about 500 rpm, will return to normal upon placing the car in neutral again. Egr and iac have been cleaned, new intake tube has been installed, and car is completely stock. Also have a whining/whistling sound at lower rpm
 
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