I think you are stretching things a tad. There are some difficulties at Whitechapel but action has been taken to pull things back. I don't get any sense that the core tunnel section is delayed - that looks to be on time. Abbey Wood's new station building is due to open in October this year. Custom House is done and being fitted out. The DLR station is getting a capacity boost now. Canary Wharf is finished. I understand Liverpool St / Moorgate is proceeding well below ground but I haven't see how Moorgate's surface works are going. Farringdon also seems to be romping along as is TCR despite issues with an over station development at one of the ticket halls. Bond St also seems to be OK as the Crossrail station is done and the LU works finish later this year. I'm less sure about Paddington where there are rumoured issues about fit out.
I understand the tracks are all in place in the tunnels and cabling and catenary work is underway. I think the game plan is to give the operators about 8 months to test trains and systems at stations.
A paper on transition issues when to a TfL Cttee meeting last week.
https://tfl.gov.uk/cdn/static/cms/documents/pic-20170628-item16-elizabeth-line-transition.pdf
The stations on the eastern branch to Shenfield are in varying states of rebuild and with new lift towers and overbridges being needed at some locations. No sign of work starting at Ilford yet.
Network Rail would appear not to have covered themselves in glory with the news about the western stations. However we do not know exactly what the issue is as they won't tell the media. It can't be funding because Crossrail works are ring fenced and there is a separate agreement between TfL and NR to progress these works. Given there is no great increase in frequency when TfL Rail take over the Connect service next May I'm not quite sure why everyone is having 57 kittens about the delay until 2019. Yes it would have been lovely to have new stations completed this year but what would the point be as there is no Crossrail service until Dec 2019.
I am surprised NR have not learnt from the GOBLIN debacle that it doesn't play well in London to not tell TfL / the Mayor / London Assembly / local politicians what's going on. It rather makes the generally very slick Crossrail PR / stakeholder management process look a bit "poor" (understatement). I expect this one is going to rumble on and on until NR come clean.