Here is what Aaron at EMI said about swapping from BT40 to CT40:

"There is way more involved in that. We have had our serviceman do a swap once and between parts and labor (you need a service man very familiar with this tool changer setup) it was well over a $6000.00 event and this was in 2010. That is not a project we would recommend taking on. In fact, you can buy a used Bridgeport machining center ready for CT tooling for the cost of what it would take to change from BT to CT."