The line that has same stops as the bakerloo line is the Irt Flushing 7 train at 23 stops. BKL has 25 stops.
The L or 7 are really the only ones you could do as they are fully self contained. The other lines all have inter-running with other lines and it'll very quickly get complicated
You mean Queens Boulevard 6th Ave 8th ave BMT Broadway. During late night service patterns 6th Avenue Queens Boulevard still have Express services D train 6th ave and 8th ave 59th-145th street stations express. Queens Blvd F train express 24/7 E Train local daytime Express.
The 7 line would be great; Flushing, Queens all the way to Hudson Yards on the west side of Manhattan. You might even catch a glimpse of (generic ballpark that is in no way affiliated with the Mets).
During the late night hours you mean or normal service pattern. I'm only familiar with Flushing 7 train Lexington Avenue 4 train IND 6th ave D & F trains BMT Broadway N, Q & R trains. Important thing to remember is this Q train Express stops at 10:30pm runs local to 96th st 2nd ave past that time while Lexington Avenue 4 train Express runs till 12:am