See also in the Sportsterpedia;

• Removing the Rocker Boxes
  
• Rocker Box / Rocker Arm Inspection and Servicing

One issue in installing the rocker box is that it has no alignment method. ¹⁾
Basically, every time you put it on, it's in a different place.

When installing the rocker boxes, be sure to put them on with the engine positioned such that the cams aren't trying to open the valves. ²⁾
Else you can damage parts.

Middle rocker box:
The 86-90 doesn't incorporate the area were the umbrella flapper valve would go. ³⁾
So due to functionality, the 86-90 mid section won't fit 91-03 boxes.
But the 91-03 middle cover will fit 86-90 boxes.

The FSM details the proper installation sequence of the bolts.
Installing the bolts in the proper order prevents potentially warpage of the cover(s).
It also mentions making sure that both valves are closed prior to removal.

On assembly, it's even more important to slowly tighten things in the proper order to allow the lifters to bleed down.
(prevents things like bent push rods and destroying the cam bushings).
Also, make sure you can spin the push rods BEFORE turning the motor over the first time.
Obviously, you can skip these steps and get lucky.
But, why? Just follow the manual, it's easy enough to do correctly.

Below are pictures of the lower rocker box.
The circled areas are where the bolts would be:

On assembly: ⁴⁾

• Work in this order. Blue→red→yellow.
  It is suggested to do this slowly (one turn at a time) and for the blue ones to do it in a cross pattern.
  This is to bleed the lifters properly.
• An easy way to remember the order is to work from the larger bolts to the smaller ones.

Torque values:
Installing the bolts in the correct order doesn't take much longer and saves some potential headaches.
While many experienced guys won't use a torque wrench on the smaller fasteners, it is suggested to use one.
It doesn't take much to strip one of these for new or experienced mechanics.

• Blue - 18-22 ft-lbs
• Red - 135-155 in-lbs
• Yellow - 135-155 in-lbs

91-03 style lower rocker box 5)	04 and up style lower rocker box 6)