The LRV currently favored to replace the Dinky is simple enough to be maintained locally, and a spare half-unit will be waiting in the maintenance depot. In addition, the university's Tiger Transit currently operates a bus to the Junction in redundant, parallel service to NJ Transit's EMU service, previously protected by an NJ Transit bus. Contingent backup service is absolutely no problem whatsoever, period.
As for platform level, why not just go with the simplest solution? The platform at the Junction will be replaced with a low-level platform. All new stations or stops will be low level, fully compatible with the low-floor LRV.
The proposed extended route to Nassau Street will go from the new station around the new Arts Campus just inside the existing roadway on a dedicated ROW and on up University Place in a dedicated lane, now parking, which will be moved to the opposite side of the street when the street becomes one-way.