are you gonna take all the 5 modes of transport? if yes, then pass is still cheaper than individual. if no, then you calculate if the few rides will exceed the cost of the pass or not. if never exceed, then just buy one way tix. Hakone Transportation Guide | Transportation | HAKONENAVI
Not sure about the operating hours but for the pass, you can buy in advance from the ticket counter at the north side of Shinjuku station. I think the tourist counters should be selling them or they can at least show you the directions. The station can be very confusing for first-timers.
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