The beam should strike and leave each mirror at 90 degrees, the chances of any mechanical item being 90:00:00 is pretty much a non starter so its a case of the best available.
If tube to mirror 1 is as near 90 degrees as possible then its a train to get the rest of them as close as possible.It will never be perfect (the fact the slidways move prevent perfection) but as Tweaks said its the final mirror to lens that really matters. So long as the entire beam is encompassed by the mirrors and is within a small margin of 90 degrees you wont get too many problems.
The main problem to avoid is beam scatter, anytime any part of the beam strikes an object in the optical train you will lose power, so long as the final exit of the beam is in the correct verticle plane it will work fine
Have a look at Tweaks photo, if your beam is doing that then you won't have many problems
best wishes
Dave