There are some caveats for using extended range vlans range 1024 - 4096.
Versions of Cisco Catalyst OS 6.1 and IOS or newer support 4096 VLANs using 802.1q trunks, but if i remember correctly VTP and ISL on trunks isnt supported in this range.
Id want to clarify this but the 1024 limit applies to mac addresses entries not vlans so you should be ok.
Im not sure how much of this your already aware of so please forgive me should you have already seen the literature but please see the snippet below.
STP MAC Address Allocation
Catalyst 6500 series switch chassis have either 64 or 1024 MAC addresses available to support software features such as STP. To view the MAC address range on your chassis, enter the show catalyst6000 chassis-mac-address command.
For chassis with 64 MAC addresses, STP uses the extended system ID plus a MAC address to make the bridge ID unique for each VLAN.
When the extended system ID is not enabled, STP uses one MAC address per VLAN to make the bridge ID unique for each VLAN.
If you have a network device in your network with the extended system ID enabled, you should also enable the extended system ID on all other Layer 2 connected network devices to avoid undesirable root bridge election and spanning tree topology issues.
When the extended system ID is enabled, the root bridge priority becomes a multiple of 4096 plus the VLAN ID. With the extended system ID enabled, a switch bridge ID (used by the spanning tree algorithm to determine the identity of the root bridge, the lowest being preferred) can only be specified as a multiple of 4096. Only the following values are possible: 0, 4096, 8192, 12288, 16384, 20480, 24576, 28672, 32768, 36864, 40960, 45056, 49152, 53248, 57344, and 61440.
If another bridge in the same spanning tree domain does not have the extended system ID enabled, it could win root bridge ownership because of the finer granularity in the selection of its bridge ID.
