So West Medford is a major problem to increasing service on the Lowell Line - eventually you start getting enough Lowell locals and Haverhill expresses and Downeasters and maybe NH service that 60 will be a constant mess.
So my proposal: demolish the Dunkies, the liquor store, and take the one tiny double-decker off Circuit. Built a curved overpass that doesn't ruin the little downtown area. Playstead turns down the former 60 alignment to Canal Street.
That's gonna make a fine mess of the place. It's a square with 5 converging bus routes, dense-ish sidewalk retail, and a fire station. I really don't think you can disrupt the street grid like that, engineering-possible or not. How would such a similar thing fly in [insert square here] in Somerville instead? I doubt it...it would get destroyed during community input, and for defensible reasons.
I think the only way grade separation works is:
1) Sink the tracks into a pretty steep dip coming off the Mystic Bridge. 1400 ft. of running room off the bridge before it has to level out under Route 60. 1.5 or 1.7% grade on the Mystic side, closer to 1% on the outbound side. 1.5% gets you to 21 ft. depth by the time it has to level out, adequate 100-year clearances for double-stack freight with no electrification or autoracks with electrification. 1.7% gets you 23'8" depth, future-proofed for double-stack freight under electrification. Note that this is better than the following commuter rail grades: Wellington tunnel on Haverhill/Reading (3.5%), Neponset bridge on the Old Colony (3%), Mystic bridge on the Eastern Route (1.6% Somerville side / 2% Everett side).
2) Bridge over Canal St. with equal roadway rise to the tracks' fall by that point in the incline.
3) Retaining walls poured to the ROW property lines so it is 4-track width and can take a GLX extension someday from Route 16.
4) After crossing under Route 60, widen out the cut a little bit more so you can do ramps down to the platform. Island platform probably works best. Regs are for 5' minimum unobstructed platform width (add extra cushion from there for benches, signage, etc.), although with an island having center signage and shelter supports and whatnot that probably means 10-12' width to meet the unobstructed regs. Cut has to future-proof for a rapid transit station
displacing a commuter rail station, so make sure width is such that it can fit 2 thru commuter rail tracks and 2 island station GLX (or HRT) tracks at 6 cars' length. Which probably means you can do an 800 ft. full-high island commuter rail platform with 1 freight + Downeaster passing track off to the side, and still have a little slack space along the walls. Have the cut narrow the slack space to the north as it passes the 6-car threshold for whenever that becomes an RT station. If/when the station flips modes you'll be able to lop off some platform length and return that to just track space.
4a) Let's assume that the ugly-ass Rite Aid is history and there's a little bit of intersection realignment and air rights to tap. Let's also assume that if something clearance-wise in the cut needs adjustment there's play room for a 1-2 ft. 'hump' in Route 60 and the aligned intersections, which could nuke the Dunkies if it has to (I'm gonna take a wild guess that Dunkies is too-prime a property and will get redeveloped).
5) Can be constructed by doing one single track shifted to far west side of ROW (aligned with
this maintenance-of-way siding), temp mini-high platform in the Rite Aid parking lot, and soil stabilization to dig two-thirds of the trench. Then shift single-track into the trench (may need to close station entirely or do a 1-car mini-high out by Playstead Park). Finish the other wall of the trench, pour platform, install second + passing track. No service disruptions except for the temp platforms, no freight disruptions.
That preserves and improves the square, eliminates the crossing, and future-proofs it for all height and width clearances for: tallest/widest freight under diesel, tallest/widest freight under electrification, GLX rapid transit extension displacing commuter rail station, and HRT conversion of GLX + extension displacing commuter rail station.
Pricey. But it's a 100-year solution you don't get by warping the street grid or building an ugly-ass ultrawide viaduct blotting out the sun over the square.