You do not need to separate the E&M T1 into an incoming / outgoing group. You can use one single group for both.
For the 2nd issue:
PBX-1 -- T1 E&M -- UC520-1 --- H.323 VOIP --- UC520-2--T1 PRI --- PBX-2
You can make calls from PBX-2 to PBX-1 but not the other way? Do you have IP phones at any of the UC520? If so it may be worth trying to see if the you can call from PBX-1 to an IP phone on UC520-1 (same UC520) & call from PBX-1 to an IP phone on PBX-2 to help isolate if the issue is local or remote. This would require looking at your config in depth and perhaps even debuging - a TAC case maybe the best option.
An app note on Multi Site - note this is targeted towards IP phones on both sites that may help:
Configure Multicast Paging on the Cisco IP Phone 7800 Series or 8800 Series Multiplatform Phone
The Cisco IP Phone 7800 and 8800 Series Multiplatform Phones provide voice communication over an Internet Protocol (IP) network...
Add Call Park on a Cisco 7800 or 8800 Series Multiplatform Phone Key Expansion Module
Call park allows the user of the phone to put an incoming call on hold so that the call can be retrieved on another phone. A call is park...