I had a similar problem when I drilled my nanocube. The hole was maybe 0.8mm too small to fit the bulkhead completely in.
Used a dremel bit just like this (see below), and went to town. I ran the tool around the hole, against the rotation direction of the bit .... and kept just going around and around quickly. I can be done dry, and it only took about 5 minutes per hole to get a perfect fit.

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28g Nano Cube drilled with 13g sump in stock stand. Vertex IN80 Skimmer, Phosban 150 Reactor, Apex Controller, DIY LED with stock hood, dimmable
Established March 2006
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