I am building tamiya's old PZ IV Ausf d and adding teh applique armour to teh side and front. My quetsion is should there be a bit of space between this extra armour (specifically the side armour) or should I fill it in so there are no gaps. My meager refrences do not show a top side view.

I would have to say no space because this is what I found on the Pz IV:

New features on the Aust D included an external gun manlet, with 35mm armour shield, a gimbalmounted hull machine gun in an armoured mount housing, and a distinctive staggered front superstructure with the driver set forward. While this was the basic Pzkpfw Ausf D of 1940, there were many later retrospective modifications, and these included the fitting of anew pattern drive sprocket, wider tracks longer tracks and extra armour (30mm front, 20mm sides) in the from of plates bolted to the superstructure.

Kencelot is right the armor was bolted on so there should be no space.

The added armor plate on the superstructure sides was bolted directly to the existing armor plate. The extra armor plate added to the front of the driver and radio operators stations was spaced off of the these locations.
See "PzKpfw IV in action" by Squadron/Signal publications "Armor #12", page 11 & 15