I think you mean Kennedy station, not Eglinton East station. No that was always part of Crosslinx - likely because of the simple delineation between the two projects at Kennedy (BTW, I was at Kennedy this evening, at the east end of the station ... coming from the GO train. The connections from Line 2 to Line 5 there look like there'll be really quite good, for two parallel(lish) lines. I thought it was Eglinton and Eglinton West (aka Cedarvale) stations that were going to be contracted by TTC.
I believe there was extensive discussion about it a thousand or so pages up the thread. The only question in my mind, is did that change take place before or after the Crosslinx contract was tendered.
From the south side of the Leslie/Eglinton intersection? What's the issue there? That section all looks finished.