pre-filter air bubbles???

My 300D-t had been idling rough and had reduced power until I replaced the leaky hand pump, this morning (I strongly believe it was allowing air bubbles to get into the injector pump - or at least wouldn't bleed the system properly). It idles smooth, after starting, now and power has been restored. HOWEVER, there are air bubbles in the pre-filter that I cannot rid of. Is this normal? There are NO more bubbles in the clear lines from the fuel filter to the injector pump; should I just not worry about bubbles in the pre-filter?
Let me know what you guys think. Thanks...