2000 ford taurus rack and pinion install

I have taken my rack and pinion out of my Taurus and I got it on the bench and before I took the measurements for proper alignment into the steering knuckle I noticed the the boot on the passenger side was compressed and I pulled the shaft to decompress the boot my mistake I should have left it alone. I need to know what the correct procedure for putting rack and pinion and steering knuckle in the proper position. I have measured the threads on both pinions if that will help.

What kind of working conditions do you have there? i.e., level concrete floor? Covered from the weather? Is the car currently on jackstands or ramps or jacks?

That begs the question, why would you remove the rack from your Taurus? It’s certainly not a fun job.

I’m also curious about the reason for a rack removal other than replacing it.

That being said, center the steering wheel.
Turn the steering gear all the way to the left. Turn it all the way to the right while counting the number of turns. Turn it half the number of turns back to the left and that should put you in the ballpark.
No matter how carefully this is done the toe needs to be properly set any even if you had not inadvertently moved the rack. The act of taking it out of the car causes a variation.