If you current system is suspect, document it well. Then consider a blue seas or other universal fuse/relay/distribution block. Whether its worth it or not depends on the complexity of the wiring, available space etc.
A higher output alternator may require more current on D+ to start charging. Each alternator design may have different numbers of windings in the secondary coils. If you have a high resistance (poor connection) anywhere in the D+ circuit (light, cluster, or to the battery), then that may be the cause of the issue.