Hi, 110ryan,
If you're set on building your own, I recommend making a drawing first, it's what I do when I build a piece of furniture. As far as glass goes, I'm still not proficient at cutting it cleanly, so I order panes to measure from my local glass supply company (eg, a place that makes replacement panes, as part of its business of installing and repairing home and business windows).
However, I saw a really neat tip a couple of years ago, in an online build of the Trumpeter 1/350 USS Hornet: Use a baseball bat display case. You should be able to get them through your nearest sports collectible dealer; if he doesn't have any on hand, he can probably order it. Or search the 'Net for one. But the prefab bat display cases are perfect for ships in 1/350 or 1/700.
Happy modeling!