I think it’s possible to achieve everything you want.
You can terminate your T1 on your FreePBX server via PCI card or using a PRI gateway (Sangoma, Digium, Adtran, etc…).
You can connect your faxes to FXO/FXS cards in your server or use a gateway for that too.
If you got sufficient bandwidth, you certainly can run calls between your buildings over the site-to-site VPN.
How is your T1 currently connected to your PBX?