Wrong on that assumption...
Dray cost into central Mass from central Maine is typically about $500 - $700 per van truck load depending on capacity.
Per intermodal LOAD (costs are by load not by hour), typical dray cost less than 50 miles is no less than $250 (I've seen it more like 285-325). Since intermodal is dray - rail - dray, we assume at least $500 per load goes to the trucking company getting the container to and from the rail. Assuming the RR is cost competitive with the trucking company, lets say its $700 in gross revenue a container - $500 to the trucker. Leaves $200 per container to work with which at a train of 60 containers is $12,000 in revenue to the RR.
Been taking about 3 crews to operate @ 12 hours each @ $25 per hour per person (very conservative on that) times 2 people = $50 per hour time 36 hours = $1,800 fix labor cost for rail transportation. RR has to pay to load/unload the entire train, probably a crew of 3-4 guys working 12 hours each (lock/unlock ICBs, check paperwork, inspect equipment, ect), we assume at least $20 an hour. $80 per hour for the crew times 12 hours to load times 2 for the unload = $1920.
Fixed labor per train is about $4K
Locomotive fuel tank carries more than 3,000 GAL of fuel, assume we burn half a tank each. I don't know enough about this so maybe I'm way off but lets assume 4 GP40s @ 3,000 GAL each and we consumer half the fuel to move the train = 6000 GAL consumed at avg diesel fuel price of $2.54 = $15,240 in fuel (assume there is a fuel surcharge per container, might kick in a few Gs to this) so lets call fuel $12,000 after FSC.
So to load the train, get it moving (probably a 4th and 5th crew for switching, maybe some carknockers, paperwork, dispatching, ect needed too) is a fixed cost of about $1800 + 1920 + $12000 + $2000 MISC or slightly more than $17,500. Conservative estimates on my part again, on this RR its probably more like $20K just to get the containers moved from terminal in WTVL to terminal in AYER. That means you gotta be making $333 per container to break even assuming you give the trucker $500, which means you charge the PS about $850 per container which could get me a truckload from Maine to PA or Ohio no problem.
Oh, and you run the train again back to Waterville completely EMPTY. So whatever your fixed cost is to operate is doubled for the entire service so $34,500 per round trip, so you got to make slightly less $600 per container to COVER COSTS, which is likely $1150 - 1200 charged per container to PS. That equivalent gets me a truckload to Chicago/Wisconsin OR a Boxcar from Waterville to Worcester with 4 times as much tonnage in it.
A few things I think:
PS is NOT paying $1100 - $1200 per container, probably slightly more than a truck dray. We really don't know but I'd guess more like $700-800.
Pan Am thought this was good PR plus would springboard intermodal interest with other shippers, some who have tried it but never gotten past trials.
Without expanding the service either A.) Into a new market or B.) as part of an existing NS or CSX service, it won't succeed.
Building density for shippers beyond 50 miles from Waterville will be tough, average rate per mile can be $.90 to $1.00 on a spot rate plus the up front $250ish. If you contract a rate with a trucker, you might be able to get that down but you need to guarantee them volume.
Remember, the fixed costs remain the same so adding train density and reducing costs are both key. For Pan Am, the cost reduction is going to be much easier to control than the freight market... I would try to reduce number of crews to move the train, use more fuel efficient locos (C40s?), and tie into another RR's network to attract IMCs so you can build density AND reduce the cost of operating two terminals (load at your own, unload at another RRs terminal).
EDIT: I also forgot the container/chassis lease costs. Chassis is usually $10-15 per day. Cycle time would be 3-5 days. No idea about the container. 60 chassis * 10 * 3 days on the road * 2 drays = $60 in chassis fees per container. Once again, no idea how much the lease would be on the box from Eimskip.