If you don't want to invent a IPv6 RA and DHCPv6 server, you could autogenerate rtadvd and dhcpv6 configs, but I don't know if that would be okay (considering you'd have 1000 rtadvd + 1000 dhcpd instances for 1000 clients). I am attempting to add IPv6 hooks using the said approach on a fork: https://github.com/neelchauhan/mpdx Keep in mind that this fork is far from complete and happens in my spare time, since my $DAYJOB isn't in networking or FreeBSD. And even in my free time I spend more of it...
[Feature Request] PPPoE/L2TP Server IPv6 Address Assignment + DHCPv6-PD (not IPv6CP)