Phase 1: I figure elevating Eglinton is pretty much mandatory and the cost would be about $300M to $400M on top of the LRT plan. Add another $300M to extend the SRT to Malvern and not stop one station from the end.
Phase 2: To have a branch of the line continue north parallel to Kennedy, the corridor is not wide enough. 2 tracks would be needed for GO and 2 for the LRT. From Sheppard to Finch it is very residential (single family) so I will assume for now that it would only go up to Sheppard. That is about 2km and the line would have to be elevated, going over Progress and the 401. Lets say another $300M to $400M for this.
Phase 3: To have a line go from Agincourt to U of T Scarborough would require say $200M for an interchange to facilitate the Southbound to Eastbound and Westbound to Northbound movements. It would also require about 4km of elevated track @150M/km to get to U of T ($600M). This line would be about $800M total.
In total, these would add up to $1.8B - probably similar (if you use a high estimate) to the extra required to bring the B-D subway up McCowan to Sheppard. It can also be done in stages so the extra needed now is just the $300M to $400M to elevate the Eglinton LRT, which has immediate benefits and also keeps all options open for the future.