The incline could be end to end supported over Manchester Castle, not too hard in the world of steel, and the land between the two viaducts doesn't really require any 'in keeping with' as it's already got half finished building developments that have been abandoned. If the Altrinham Lines were handed back over to Heavy Rail, then you could justify the inital re-opening with all the major trackwork and new bridges in the reigon of Cornbrook Interchange. Taking longer distance or express services off the Chat Moss route (that don't stop at Paitcroft or Eccles), it would be possible to re-open the line from Glasebrook to Kenyton with some new junctions onto the Chat Moss Route, with a 4tracking of the CLC route to said junction would mean that 2tph Central - Liverpool L St (All Stations) and 2tph Central - Glasebrook - Wigan N Western would be entirely possible. (With associated electrification of the CLC) That would make it back into a proper commuter line, and provide a diversion away from the Chat Moss line through eccles to Central and Oxford Road, be it needed without much of a time penalty, if the CLC has it's fast lines of the 4 track at 100 or 90mph. slows at 75/90.
The only complicated parts are of that would be some of the 4 tracking from Cornbrook Interchange to Glasebrook East Junction, and moving some things aroun at Cornbrook, slewing the metrolink lines on the viaduct to fit 6 track on the two viaducts again, met in the centre of the two NR routes, a small amount of platform moves at the Deansgate Castlefeild metrolink station, and a shiney new walkway to the Central Concourse, or an additional set of Metrolink platforms at the front of the Central Concourse. Taking services into Central from the Windsor link is expensive but not do-able, but running them through Victoria and Philips Park would mean more services could be sent into victoria anyway, without having to add more platforms. Basically configure services at Victoria so that nothing terminates from the West, currently (feel free to correct me on this) 4tph from Bolton 2tph from Atherton and 1/2tph from Eccles, one already continues to Rochdale anyway, adding in some West Facing bays would mean more could be sent up to Rochdale, say 3tph, 2tph could then be sent to Stalybridge, would need some trackwork at Stalybridge, but yet again, not that difficult to do. A slight bit more difficult would be starting passengers services cross manchester via Philips Park to Ashburies, but yet again, not too hard to acceive, re-signalling with better headways, new station at Sportcity for Metrolink Interchange and two or four new platforms at Ashburies to terminate services at, and allow them to run through to other parts of East Manchester and North Stockport (Rose Hill Marple - Victoria - Atherton - Wigan Wallgate) for example. Aaaanyway, off topic massively now.
I've seen somone mention a Manchester Bypass for HS2 some time ago, where Manchester would be on a loop for HS2, this sounds like a good idea as linespeeds in Manchester will have to be reduced for either tunnels or tight curves, and if if where on a Loop, say from either Crewe or Manchester South Parkway to Manchester North Parkway or Preston, depending on the size of the loop. Say it ran from Manchester South Parkway (Manchester Airport) to Manchester North Parkway (Horwich Parkway area) with the stations located on the junctions, if the previously shown inferstructure where employed at Manchester South Parkway, allowing services to run either from north or south into Manchester on the southern approach, and had a Manchester West Parkway station built, so long as the bypass route where built as 4 track, a new station at 'Manchester North Parkway' or Horwich Parkway area, could be built as a terminal station, with the mainline running through, and 'Javalin style' services run for Manchester Commuters, With appropriate motorway Junctions at the M61 (already there, Horwich Parkway and Middlebrook), M62 and M56 (Already there, Manc Airport), 3 extremely large parkway stations could be built, with even the possibility of a 4th or 5th at Bolton Town Centre, next to the Bus Station and Train Station (spanning the two), there is kinda enough space to slot the track through and out toward the old M601 alignment to access Central Manchester, this means there could be a new motorway spur between Junction 16 and 17 for 'Manchester East Parkway'. This would mean the Central Manchester station having to have some through platforms, there is space to route a new viaduct through the city centre, albeit at low linespeed, and it would need to dive into a tunnel near Oxford Road station, have the incline next to the current viaduct, and make a couple of roads a bit narrower, or, build it up higher, to fly over all other lines at the Central throught, double deck it with the line from Deansgate to Ordstall Lane and either keep it at high level over the A6, Crescent, through the Salford University Campus and onto the M601 alignment. This would all need to be built a level above the current castlefeild viaduct, and climb an additional level to clear the metrolink lines and any additional lines into Central that could be built later, an alternative would be to run through Victoria, if all standard services from the East ran through the station, then the High Speed lines could run through part of it, this could mean, running the HS lines from, say Piccadilly South (Mayfeild terminus) out toward Philips Park, basically doing a U turn, re-instating the 4 track through there and around to Victoria, at HS linespeeds this would only take 2 mins, also crating a fast link to Victoria, splitting the remaining heavy rail platforms and providing a centre road could mean being able to still terminate some services from the west, add some west facing bays if needed. then follow the trackbed on the level through Salford Central, removing (or using) platforms 1 and 2 for the HS lines, use 3 and 4 for standard services instead. That would provide a link taking say 5mins from Piccadilly to Crescent (only the same as currently, but possibly much cheaper as there is no tunneling needed). If all this could be put in place then with a through line at piccadilly a service pattern could be in a Loop to provide:
Manchester N Parkway - Bolton T/C - Manchester E Parkway - Manchester Piccadilly - Manchester South Parkway - Manchester West Parkway - Manchester North Parkway
Or the one way terminal with loopthrough at Victoria would provide a service pattern of...
Manchester N Pway - Bolton T/C - Manchester E Parkway - Manchester Victoria - Manchester Piccadilly
AND
Manchester N Pway - Manchester W Pway - Manchester S Pway - Manchester Piccadilly each to be 4 or 6tph
I know providing a station at Bolton might sound silly, but a lot of passengers do interchange at the station onto piccadilly services, so it makes sense in my world. I'm estimating journey times at, from Piccadilly
Picc - Victoria (3mins) - Manc E (7mins) - Bolton (10mins) - Horwich (15mins)
Picc - Manc S (7mins) - Manc W (13mins) - Manc N (17 mins)
Rant over, I hope...