Here is a standard route for 106% with heavy naija usage.

Forest: 1-1 - 1-20 (Meat boy)

Dark Forest: 1-1x - 1-20x (Meat boy) Farm 1-18 (Meat boy)

Hospital: 2-1 - 2-20 (Meat boy)

Factory: 3-1 - 3-3 (Meat boy) 3-4 - 3-7w (Josef) 3-1x - 3-4x (Meat boy) 3-5x - 3-7x (Josef) 3-8 - 3-13 (Meat boy) 3-14 - 3-16w (Josef) 3-17 - 3-20 (Meat boy)

Dark Hospital: 2-1x - 2-3x (Meat boy) 2-4x - 2-5xw (Josef) 2-6x (Meat boy) 2-7x - 2-20x (Naija) Farm 2-10x (Naija)

Dark Factory:
Farm 3-8x (Naija) 3-8x - 3-20x (Naija)

Hell: 4-1 - 4-20 (Naija)

Rapture: 5-1 - 5-7warp (Naija) Skip 5-1warp Exit and reenter 5-7warp to get to 5-1warp 5-7 - 5-20 (Naija)

End: 6-1 - 6-5 (Meat boy)

Light Cotton: 7-1 - 7-20 (Meat boy)

Dark Cotton: 7-1x - 7-20x (Meat boy)

Dark Hell: 4-1x - 4-20x (Naija) Farm 4-9 (Runman)

Dark Rapture: 5-1x - 5-20x (Naija) Farm 5-16 (Runman)

Dark End: 6-4x - 6-5x (Meat boy) 6-1x - 6-2x (Meat boy) Farm 6-3x (Meat boy) Dark Fetus (Meat boy)

¤Do the level and replay for the warp ¤¤If you get glitch girl in a level where there is a warp zone, meat boy will be placed on the warp after exiting or completing the glitch level

Get the warp during the section unless otherwise mentioned. If glitch girl appears before the farming section the farm is obviously not necessary.

Possible route improvements:

• After 3-7warp go to 3-5x instead of 3-1x, do 2-7x with meat boy and do 3-1x after naija is unlocked (saves 5+ seconds)
• 3-11 - 3-12 with Josef (saves ~5 seconds)
• Do 5-1warp normally with naija (saves up to 2 seconds)
• Skip 3-16warp when doing factory. Do dark factory after you have completed dark hell and dark rapture, do 3-16warp with steve after 3-20x (Saves 5 seconds but introduces a possibility to crash the game (machine dependent))

Other reasonable route changes (not all are compatible with each other):

• After finishing 2-8 go to 2-5x warp and do rest of light hospital. Do the whole light factory without completing any dark levels. Next do 3-1x - 3-8x warp. Naija will be unlocked, use her to complete rest of dark factory. Do the rest of dark hospital with naija and continue to hell normally. (Saves ~10 seconds to the given route, disallows 3-8x farm and doing 3-1x with naija)
• Chapters from dark factory to dark rapture can be reordered (no or minimal time loss)
• Farm in 3-11x instead of 3-8x (loses about 5 seconds on average but makes terrible farms less common)
• Farm 4-9 with either naija or meat boy (makes the farm slightly slower)
• When doing rapture skip 5-1 and 5-1warp. Do them when doing dark rapture (loses ~0.25 seconds but allows a possibility for 5-1 glitch girl saving 10+ seconds
• 5-3x with runman (slightly faster unless the fast strat in 5-3x is used with naija)
• 5-7x - 5-9x with meat boy (~5 seconds slower)
• 5-10x - 5-11x with kid (~5 seconds slower)
• Farm 5-3x with steve (slightly slower than 5-16 farm)
• After dark rapture do 6-1x - 6-5x + dark fetus and farm 6-2 (on average 10+ seconds slower but makes the farm less risky)