MOM's original concept was to relieve traffic congestion on the US-9 and possibly NJ-18 (to New Brunswick) corridors. Hence the original preferred routing through Monmouth Junction. The other routes via Red Bank or Matawan could relieve some congestion for riders with N. Jersey or NYC destinations. The Mon. Jct. route will most likely never be built do to NIMBY attitude in North Brunswick, Jamesburg and Manalapan. (The latter 2 don't even like the twice weekly 10 mph freight trains.) The route through Freehold to Matawan has the same NIMBY situation in Manalapan and Marlboro. So the only viable alignment is through Red Bank. This only relieves highway congestion from the lower part of US-9, but would still be beneficial to residents of northern Ocean and western Monmouth counties.
So here's another solution to US-9 traffic pollution:
Rebuild the CSao Southern Secondary to FRA Class 3 or 4 and add some passing sidings.
Build stations at necessary points.
Buy some FRA compliant DMUs.
Run trains Lakehurst to Red Bank.
Layover in RB in NJT MoW yard and in Lakehurst on the Navy spur. (add more spurs inside the base as necessary) The added maintenance costs of the DMUs could be offset by removal of some of the Lakewood - NYC buses.
Freehold - Red Bank service via Farmingdale could be added later further reducing US-9 traffic. The former PRR station in F'Hold is currently a NJT bus stationand is run by a private contractor. It could be re-furbished to a full NJT rail/bus station. Layover and room for another commuter park/ride facility could be created in the farmland just south of Iron Mountain (formerly Brockway Glass) on Business NJ-33. This would have much better highway access than Freehold Center. The rail turn-out for Brockway still exists, but could be made into a wye. DMUs from Freehold Center could stop at the park/ride, engineer changes end while loading and then continues on toward Red Bank. The biggest problem in downtown Freehold even before any rail service is parking. Build a parking garage with the borough sharing the cost.
North Jersey Coast line trains could have cars added on those trains that would interchange at Red Bank. No additional trains on the NEC or into NYP. The overnight layover yards at Lakehurst would only need cleaning, water, sewerage and minimal servicing capabilities. I don't know if NJT has fueling capability in RB, but that's easily fixed. DMUs could fuel up there while waiting for the next south (RR west) bound NJCL train. The only bottleneck I see is NYC/North Jersey bound passengers would have to get from the west platform to the east platform at Red Bank because the DMUs would only have access to the west platform. (due to track configuration) A covered pedestrian bridge or tunnel would be nice.
All of the above would be much lower cost to NJ taxpayers while gaining the highest possible ridership and improving the US-9 congestion. Also much more environmentally friendly. 1 single-level DMU car could take 100 cars or 2 buses off the road. Extending the southern terminus from Lakehurst to Toms River could gain even more ridership and reduce some GS Parkway commuter congestion. The whole project HAS TO BE time competitive with highway travel for commuters to use it at all. High running speeds and as few stops as possible would be necessary.