Increase benchRun time to improve reliability of bench_test3.js

(cherry picked from commit 689e23eace05079e4db58ea92caff2aafb1c75db)
Increase timeout of replSetReconfig to leave time for initial sync in two_initsync.js test

(cherry picked from commit 298470d138e0596c0f61fff46cbada3bf402a846)