I don't believe the remaining sections of Finch, Eglinton, Sheppard and the SRT are covered in the next wave,
http://www.bigmove.ca/what-were-building/the-next-wave
they aren't, and will be something that the city would have to fund if they wanted them any time soon. and quite frankly, all but the eglinton extension are relatively small projects that could be funded over time with the huge chunk of change the city will be receiving from the 25% number. what I would like toronto to fund with those funds is:
1. Viva style BRT light on the busiest routes, this could likely be done with around a years worth of funding
2.queens quay streetcar extension, this is a key portion of the don lands but is expensive as hell at around $400 million. the bullet must be bitten though, and get done with. probably 2 or 3 years worth of funding for this.
3. Finch east LRT, a key missing connector in northern crosstown travel, a "missing Link", and will likely cost around $500 million. probably 4-5 years of funding then.
4. Malvern extension, probably $300 million, around 2 years of funding
5. widening of the DVP over the 401, and other highway chokepoints. reconstruct a lot of the Gardiner/DVP, and make it at least look slightly comparible to the 404/QEW that feeds into them. probably 1-2 years of funding
6. dig a one way southbound tunnel from the Allen to bathurst to alleviate congestion probably 2-3 years of funding
total time: 12-16 years
At this point a Lot of the transit problems would be fixed. I would suggest stretching the timeline out by a couple of years to allow for new cycling and pedestrian infrastructure, especially lots of new cut through paths to make the main concessions more accessible from cul de sacs.
note: I am basing my timing estimates on the fact that Toronto would get around 1/3 of the 25% of Metrolinx funding, or around $170 million a year.