Putting the bulkhead and transmission in the chassis
I highly recommend you tap all holes that will be threaded. I can't guarantee the screws will "self tap" into the printed Nylon they way they do in molded parts. For the bulkhead, the 4 holes where the shock tower mount should be threaded as well as the ballstud holes (#4-40). The holes for the transmission mounting and chassis tab mounting are cleared for #4's. Likewise, for the rear chassis brace that comes with the deluxe kit, the two holes where the tubes will go should be tapped for 4-40 and the two where it screws to the transmission are #4 cleared. The body/wing tube mount has all 4 small holes that need to be tapped for 4-40.
Take the bulkhead and the rear shock tower and attach them with a single screw: the one that is the lower left when it will be assembled on the car (see picture). Leave it slightly loose, just loose enough that it can "hinge" on that screw (it will be obvious why you do this later). Now take the bulkhead and put it's tabs up to the chassis tabs and slip a screw through each bulkhead tab and through the chassis tabs: use a 3/8" screw on the left of the car, and a 7/16" screw on the right side of the car. On the left side of the car, use a low profile 4-40 nut with a little Loctite (since these are not locknuts) and on the right side of the car use a 4-40 locknut. Snug down both sides while making sure the bulkhead is level.
Next take the transmission assembly and slide it under the bulkhead from the front of the car toward the back:
Gently continue sliding it back until you see the bulkhead screw holes line up with the top holes in the transmission case. Note that if you have rear arm mounts on the car during this process it's okay, but you may need to back the 8-32 screws out some so they don't interfere with the transmission case as it slides past them.
With the shock tower rotated out of the way, put the two front bulkhead-to-transmission case screws in as shown. Use 3/8" long 4-40 screws and leave them slightly loose for now.
Now put the two rear bulkhead-to-transmission case screws in. If you got the Deluxe kit with the rear chassis brace, the chassis brace goes on top, then the bulkhead, with the transmission on bottom as shown. With the Deluxe kit use 1/2" long 4-40 screws, without the rear brace use 3/8" long screws. Leave the screws slightly loose.
Flip the car over and screw the transmission case to the chassis. In front, use two 8-32 x 3/8" or 1/2" flat head screws in the stock bulkhead screw holes. For Stealth chassis cars use 2x 4-40 x 3-8" long flat heads at the back of the transmission case, or for 6-gear chassis cars use 2x of 8-32 x 3/8" or 1/2" flat heads. The car shown is going to use Stealth mounting. Once you have the 4 screws in the bottom of the chassis, snug up all transmission mounting screws (4 on the bottom of the chassis and 4 between the bulkhead and transmission case.
Now rotate the shock tower back so it's mounting holes line up with the bulkhead holes. Put in the remaining 3 screws and tighten down all 4. The lower one closest to the motorplate is nearly impossible to put in when the transmission and motor plate are installed and this is why it was put in initially. You can still get access to it well enough to tighten it though.
For cars using the rear chassis brace set you can now add the tubes. Use 4-40 x 3/8" long screws to attach the tubes to the brace on the back of the bulkhead and use 4-40 x 1/4" to attach the tubes to the rear motor guard of the chassis.
Last, if you have the deluxe kit with the body and wing mount, put the body mount post on the mount using an 8-32 x 3/8" flathead screw. The wing tubes should be about 1" in length and will press-fit into the mount. Attach the mount to the shock tower using 4-40 x 3/8" long screws. Mount it in the lowest position. If you don't have the body/wing tube mount and are using B5M mounts you can attach them to the tower. In this case you will need to use Velcro or so other means to attach the body to the car on the sides or come up with some other way.
From here you are ready to finish the build. Add ball studs to the bulkhead for the rear camber links. The inside holes are the same spacing as the World's rere spacing (below the wing tubes on the stock bulkhead) and the outer ones are the true World's location. On the rear hubs switch the location of the ball studs to facing the rear of the car (stock they point forward).