You dont need to tell me about Crossrail, I worked on both the design and commissioning for over 10 years and have worked on infrastructure consultancy (rail, nuclear and defence) for over 25 years.
To be honest I would compulsory purchase the land along Sheffield Street, excavate it and build a cut and cover underground station, reinstating the land afterwards and then developing it, that way you get any land purchase cost back. The passenger tunnels would only need to be around 100m to get you into Piccadilly.
As for the route without spending hours looking at it, there are areas around Trafford and Eccles where you could come out of tunnel and link in with the existing rail infrastructure. The natural corridor for a new line would either be roughly parallel to the M62 or East Lancs Rd, it might upset a few golfers but that gives all the more reason to build it there :-).
The estimate I made was 3 mins back of a fag packet stuff, but for some reason we pay consultants tens of millions to develop a number of solutions that work and then let the people in Whitehall along with politicians do their own preferential engineering based upon party and local politics.
95% of the problem with HS2 was pacifying politicians who had vested interested where the line did and didnt run, how much was in tunnel and allowing objections to run riot due to the woeful HS2 planning legislation (Schedule 17). All caused massive delays which then resulted in the budget being further blown due to inflation.
Everyone says why does it cost so much in the UK to build infrastructure, well in most of the rest of the world they draw a line where they want it and if you dont like it then tough luck, its compulsory purchased or you put up with it on your doorstep.