I have a quick circuit at work (Expensive @$$ machine), If it works and you have the IsoPro software i would try to sell it. I saw one used for $10k. Not saying that you could get this much, but... Plus could I have a copy of the software, our install cd is thrashed. I tried contacting the company and it did no good, not even a reply to say 'ha ha your stupid'.
Back to your question. If you want 5 inches of clearance I would build your gantry sides about 10 inches or so. This gives you five inches up from the base and five inches to mount your stuff in. Of course you sould go lower i guess, like 8 and have 3 inches to mount your Y and Z axis on. But if you have the controller, power supply, and software, and everything works, sell the darn thing if you can and buy/ make one, and give me a copy of the software ;