SL Rob -
Lets see if I can help shed some light on your questions....
You asked -"Didn't the CNJ have a crew (or more?) based out of Dover / Hopatcong "HO" Jct that did all the local work on the High Bridge / W&N trackage?"
There was at least a crew based out of HO to serve the local traffic up the D&R (which had the most industry), and whatever traffic was left on the MHRR. The last ore came out of Mt. Hope in '67, the last train north of Air Products (which probably saw some CR activity) was '74 (I will see if my boss remembers when the last car came out of Air Products).
Scrub Oaks Mine, just south of HO, closed in '66, but some companies may have lasted (team tracks especially) on the HB branch, and would have probably been switched by AY-2/YA-1, in earlier times known as the "ore train" Picatinny interchange (remember, the Army had their own engines) may have been handled out of HO - I have no idea when the traffic ended, however. Hercules Powder (just off Lake Jct) was probably worked from there, too.
"How far down the High Bridge did they run?"
A good question, probably at least to Scrub Oaks Mine/Ferromonte Jct, but all other traffic was probably switched by the aforementioned road job
"Did this crew make the run up to the NYS&W at Green Pond until 1971, and did the traffic on the W&N west/north of Lake Jct die after the NYS&W quit Green Pond?"
No they did not (see above), at least until the service To the NYS&W was abandonned in '72, and except for Picatinny Arsenal, I would venture to say yes, because there was nothing else to switch!
"When did service on the Mount Hope Mineral RR tracks die off?"
Well, except for the mines, there was nothing else. Richard Mine closed in "'58, and the last concentrated ore came out of Mt. Hope in '67, except for the test train of crushed stone that ran out of Mt. Hope in '74
"How did the local cars get to/from the W&N, Rockaway, MHM RR, EL interchange at Lake Jct? Did another CNJ crew come out of E-port all the way up to Dover/HO Jct and turn back or did the Dover crew run down the Branch to the CNJ Main to interchange?"
Well, before service to Pennsyvania ended, it was AY-2/YA-1, but afterwards (and I will have to dig out my train schedule book to look tomorrow to see what the symbol was) a local ran out of E'Port to HO and return
"Did the CNJ/EL service ferry cars to/from the Dover job, or did the ES99/SE98 only handle "Through" traffic from Pennsylvania? I remember somewhere that the last 98/99 train ran April 4 '76 (from a dated photo), was that the last move on the High Bridge?"
You are correct, ES-99/SE-98 was a thru job, to the best of my knowledge...There was also an earlier second EL-CNJ train, can't think of the symbol right now (it didn't last long)...The last train on the branch? That I don't know, but it had to have been made by CR sometime in the early 80's I believe from what I've been told by an ex-employee (I could be wrong, though)
"I was wondering about how the CNJ serviced this "isolated" segment of track during the pre-Conrail, post-diesel years. Thanks for any answers..."
I'm not sure what you mean by "isolated", but sure, no problem, I hope I've helped some. If anyone has more or better info, and more importantly can correct anything I have said, PLEASE DO! I have an interest in the line from having grown up in the area, but I never had the chance to see it in operation. There's still a lot for me to learn!
Car Floater
P.S. - A good article on the operation of the line appeared in the ARHS publication FD&S, Volume 9, Number 4
M.P. 28.5 On The NY Division