I have nothing to add to this thread because...looks like nothing has happened in the past 3 weeks.
I was passing thru Bay Riddge yesterday, and of course that gave an excuse to check out the First avenue work. Nothing really seems to have been done since the last updates to this thread. I can't vouch for the orange cone pile, but the future Yi-Pin siding is still unfinished, with a gaping hole in the N/B lane at that point which the rails just hang over (First Avenue N/B is closed at that point, and the detour follows the old Cross Harbor routing East up 41st and left onto 2nd Avenue. Are they still working on the sewer/water pipes there?
I don't have the credentials (under rscott) to enter the Marine Terminal (and I didn't have the guts to walk up to the guard booth off 39th and ask if I could take pictures) but I did notice dozens of vehicles parked over the 2 tracks entering the terminal from First Avenue. There was only 1 boxcar in the 50th street yards, although admittedly over the past few years that has not seem to have been a beehive of activity at any rate (if you Bird's eye view the yard in Bing, which seems usually a few years old regardless of the copyright date, there's usually 3-4 cars visible in the yard). I suppose everything moved to 65th street, which is not as goot from a railfan perspective (although probably much better from railroad operations perspective) - although looks like you can get a good elevated side view of that yard from the Belt Parkway East/bound (don't get on the Gowanus at the split unless you want to go to Staten Island) - one of the absolute few times you'd wouldn't mind being in slow-moving traffic in the outside lane.
Forgot to take 38th street to view the SBK yard upgrade progress (D'oh!), however, I did deviate out of the way north to check the former BEDT Kent Ave terminal (inspired by the BEDT page of Goldstein' Instrudial and Offline Terminal site) - the area architecturally seems rather indistiguishable from the Long Island City residental redevolpments (rather SimCity 4 like), although there were more Hipsters ambling along the streets. No real trace of the BEDT history left (yes, I realize some buildings have been repurposed), except for the 2 sections of track embedded in concrete that used to be part of the bulk flour terminal, now part of the waterfront park.
Depressing all around for railfanning - as for First Avenue right now, even with the new tracks, I am reminded of a quote from Jay Bendersky's 1988 book "Brooklyn's Waterfront Railways" (which at that time inspired me to start checking out Bush Terminal back then) - "Business has never been worse!" (I hope 65th street yard is booming, else we are in BIG trouble).