RE: Getting Error in Full sync 9999 and Health check
For the Full Sync error - open the "Initialize Commerce Scheduler" form, and select to override existing configuration. After it has initialized it then go and kick off a new full-sync, that should address the error.
For the Runtime error - this looks to be something completely different, and might need to contact support. This looks to be a local dev box (not CSU), so you can start by looking in the event viewer under Commerce-RetailServer.