Hi David,
I do not have experience with a large landscape and cross-risk analysis, but you might try Parallel Processing Configuration:
SPRO -> Governance, Risk and Compliance -> Access Control -> Distribute Jobs for Parallel Processing
Try setting to 3 processes, but you should gradually increase it depend upon the runtime and the system memory.
Regarding your question about the # of entries in the rule tables, you should look through the tables to see if there are only entries for LG's, or if there are LG entries AS WELL AS each and every system. If the latter, you can delete the access rules from the physical systems using program GRAC_DELETE_ACCESS_RULES . There risk analysis may be pulling duplicate risks because there are LGs as well as Physical Systems with rules assigned. You can always generate the rules again.
-Ken