Hi David,
Hope things are going well with you! You can only use BARS with the exact same CCM Version (including SR's), so this won't work :(
This will have to be done in multiple stages to be supported. Stage 1 will be building CCM 3.3(4) on the new Hardware (no BARS issues) then upgrading to CCM 4.1(3).If you don't want to go that way you could do the upgrade to 4.1(3) on the existing servers and then do a 4.1(3) rebuild/restore on the new boxes with the proper BARS (4.1(3)) Backup. Either way would work just fine :)
Here is a nice Step by Step Guide;
Upgrading Cisco CallManager Release 4.1(3)
Replacing Servers During the Upgrade
http://www.cisco.com/en/US/products/sw/voicesw/ps556/products_installation_guide_chapter09186a00803fd708.html#wp1039986
Hope this helps!
Rob