To clarify - this thread is focusing on a popup message (which indicates Server Connections Interrupted) that appears periodically when a Mac has a share mounted in finder via AFP (the default) to a folder on either a Time Capsule internal drive, a Time Capsule with an external hard drive attached to the Time Capsule's USB port, or to an external hard drive attached to an Airport Extreme Base station via the AEBS USB port. The popup became more prevalent after the 7.6 and 7.6.1 firmware release for the Time Capsule and AEBS - and seems to be further impacted by changes in Mac OS X as of 10.6.8 (Snow Leopard) and later 10.7.x (Lion). Some people have reported that reverting back to the 7.5.2 firmware resolves this issue. In my own case - I see the popup message on all versions of the TC firmware that I have (7.5.1, 7.5.2, 7.6, and 7.6.1). If I revert my Mac back to Snow Leopard (10.6.4 or 10.6.3) - the popup goes away - however - rather than displaying the popup - the Mac will just silently eject the share - so it the past the problem was happening - it probably just went unnoticed. OS X 10.6.8 and later seems to be doing a better job of detecting and reporting the "perceived" disconnection and now it is being noticed.
In my own experience I am not encountering any loss of data or any failures in the middle of copying files to or from an AFP share to the Time Capsule. The popup seems to be triggered only after a significant amount of data (multiple gigabytes) is copied to or from the drive - and the popup disconnect warning seems to appear a few minutes after a large data transfer (copy) has completed. At first it appeared to be tied to when the Time Capsule would spin down the drive (due to inactivity) - but closer examination disproved this theory somewhat. Even though the popup appears - the share still remains active and is usable. The popup does not occur when I mount a share on the Time Capsule via SMB (e.g. using the go-connect-to-server option specify smb://TimeCapsule).
This problem does not seem to impact Time Machine backjups at all. Time Machine backups continue to work flawlessly - and I suspect that although Time Machine is connecting to the Time Capsule via AFP to perform the backup - the popup does not occur because as soon as Time Machine completes the backup - it ejects the share - before the condition that causes the popup has a chance to occur.
I am sure that Apple will get this problem corrected - and I know they are working on it beause I have an open case for it with AppleCare - and they do periodically check back with me. This popup issue should not deter you from getting a Time Capsule - as (in my opinin) it is still the best NAS device available for reliably backing up a Mac and providing you with a dual band reliable wifi access point.
For your own scenario that you have described - I would suggest keeping one (or both) of your AEBS's and add a Time Capsule. You should keep your existing AEBS as your router (attached to your cable modem). You then want to locate your Time Capsule in an area where it will provide the best wireless access (due to the short range on the 802.11n 5GHz). You should then create a "roaming" network with your two AEBS's and new Time Capsule. You can also connect any spare USB drives to the USB port of each of your AEBS's and effectively turn them into network drives.
In a nutshell - the roaming network employs multiple wifi access points (all sharing the same network name and password) - connected to your main router (in this case the AEBS) via ethernet. Your devices (laptops, etc.) will connect to whichever access point (AEBS1, AEBS2 or TC) has the best signal - seamlessly. You would set your AEBS that is connected to the cable modem in Router mode and enable the DHCP server. You would then "create a new network on AEBS1". You would then connect the WAN port of AEBS2 and WAN port of the TC to one of the 3 ethernet ports on AEBS1. You would then configure both AEBS2 and TC in "Bridge" mode (no router or DHCP capability enabled) - and create a "new" network on both AEBS2 and TC with the same network name and password as AEBS1 (your router). Now you have a roaming network and multiple wifi access points - all appearing to be the same wifi network. To determine which or your 3 access points a device has connected to - you would need to open Airport Utility and try to determine via MAC address which wireless devices are connected to which access point.
Note: If you are in an apartment or relatively small living area - setting up a roaming network may be ineffective due to the small space. Roaming networks are more effective in larger larger living spaces where there are multiple floors where there are structural obstructions such as walls and floor where having an access point on each floor (basement, first floor, 2nd floor) makes more sense.
Something you should note: Although you can attach an external drive to the USB port of an AEBS or to a Time Capsule - and effectively create a network drive - Apple specifically states that using Time Machine Backup with USB drives attached to base stations is not supported and may not be reliable. I have done this myself (in a test scenario) and not encountered any problems - but I would rather not risk corrupting an important backup.
Here is a link describing how to set up a roaming network (and other network setups for the Time Capsule and/or AEBS). I think you should keep all your components and try to make the best use out of each.