Other thing which has a great effect on both leg vertical alignment and muscle actuation is cleat rotational alignment. In a big way.
You can't assume that both legs need the same rotational alignment.
Idea for most riders is to have the shoe/foot in a 'natural' posture for that leg - very individual to each leg of any person.
This assumes that your leg muscle actuation is balanced when your foot rotation is what it normally falls into when standing/walking/running... not always true, but true for most/many.
There are a number of ways to determine cleat rotation.
my method is now a little unconventional/old school... because I've used since my earliest days, riding with leather nail-on cleats and just modified the methodology as newer stuff was used.
I'll tell you what it is, but don;t be surprised if you don;t get it to work for you.
If it's a 'new' shoe (not replacement of same shoe model and size).
Make sure there are no cleats on the shoes. I put in whatever footbed I'm planning t use. I put oldschool rattrap pedals onto the cranks - same cheapish pedals you current get on a new bike, when you buy the bike - metal cage though... Wellgo pedals... preferrably with 'teeth'... LOL!
Put 3 layers of duct tape on the shoe sole approximately in the area where the REAR cage of the rat trap pedals might strike when the ball of foot is over the spindle.
Get on bike, go ride, get your shoes/feet placed on pedals with the Ball O Foot over the spindle. ride around the block 3 or 4 times, approx 1 to 1.5 miles, in a moderate gear where you're putting light but consistent pressure on the pedals.
In that time, your foot rotation will fall naturally to what your leg is accustomed to. THIS DOES NOT COMPENSATE FOR ANY MISALIGNMENT YOU MIGHT HAVE - DO TO Biomechanical issues, muscle imbalances, knock knee or bowleggedness - those need specific attention not addressed by this method.
Back to pedal rotation... in the short ride time, the rattrap pedal cages will 'mark' the tape (cages MUST be straight and parallel to spindle).
Peel up the front edge of tape to where you can cut the tape across the cage marks - leave the back part of the tape on the shoe.
Place the cleat onto the shoe and align the Ball O Foot to where the pedal spindle would be (you can figure that out).
Then rotate the cleat until the cleat aligns with the marked/cut edge of the duct tape. Cleats like SPD-SL, LOOK, are a very easy job to do this alignment.
Tighten screws. Go ride/test... Modify as needed. Pull off tape when you're satisfied...
Ride On
Yuri
EDIT: Not forgotten, but other BIG consideration in the whole foot/leg alignment and muscle actuation is 'Q' - can be very complicated and is very important.
ANother Ball of wax -
'What is Q factor'
'Q' is pretty much set by your equipment - but many people really need something other than what they have... and may/can/will have a great effect on pedaling performance/strength/comfort/injury for many...
also great discussion...
Want more Power (How to Respect Cycling Q-Factor)