As you squeeze the ring together and slide the cylinder down over the piston take a moment to ensure your ring ends match up with the ring locater pin installed into the piston. This you can see through the intake tract of the cylinder.

With the cylinders set into place, rotate the crankshaft and make sure the pistons freely move up and down in their bore. It should be a nice smooth rotation. Be sure to listen and feel for any abnormalities.

This next pic is not exactly correct, the y-pipe is already off. After torquing down the cylinders I realized I didn't take a pic...so this is what you get.
Here is how I do it: Mount the y-pipe to the cylinders, snug up the bolts for the y-pipe. This helps with cylinder alignment. I don't have the alignment bar or pin sets, so I do it this way and have had good luck. With the y-pipe mounted to the cylinders, install the cylinder bolts and put them in finger tight. Rotate the crankshaft over to cycle the pistons up and down a few rotations, stop with the pistons in the middle of the cylinder bore. Next torque the cylinders down in a cross pattern. Use two steps to get to the final torque setting, such as if they get torqued to 30 ft-lb, go to 15 on the first step. Now, before the final torque step I loosen the bolts on the y-pipe a bit, then torque to the final value. Then you can remove the y-pipe, because you will have a very, very difficult time getting the motor into the chassis with it on!

Next put the cylinder head on. Make sure the o-rings sit down real nice-like in their grooves on the cylinder top, or you'll get a coolant leak. I put a thin coat of black silicon on the bottom of the cylinder bolt heads, where the bolts heads contact the head (What?). This helps me in two areas, the bolts are less susceptible to loosening, and the silicon provides a little lube when torquing the bolts. Now, torque the head bolts down using the proper torque pattern, once again using two seperate steps to reach the final torque value.

One thing I forgot to mention. You can choose not to, but I always put a thin coat of either oil, or WD-40 on the threads of all the bolts, especially those points where the bolts are steel and the bolt holes are aluminum.
Install and torque the bolts which hold the seal retainer on the PTO end. These bolts get red loctite. In this pic you can see the water pump housing cover is installed.

Put on your exhaust valves.... I mean install the Rotax Automatic Variable Exhaust valves...

(Which were introduced to consumers, by the way, on the 1989 Mach 1, eh!)

Here's a pic of the stator and trigger coils installed on the Mag side. This is not tricky, the computer handles the timing, so just put them on the same way they came off. The coils I am pointing to get set in that black silicon I mentioned earlier, and the wire run behind them gets the silicon treatment as well. All of the stator and trigger bolts get a good dose of loctite. The stator bolts, if not sealed, can actually be a source of an air leak, as the back side of the bolts are open to the crankcase.

Flywheel is next. But before this I usually mount the clutch on the other side, this gives you something to hold while trying to torque the flywheel to its proper spec. Clean the mag end of the crank well, and the inside mating area of the flywheel, then put a little locite on the shaft to help keep things in place. I always use a new woodruff key for the flywheel/crank mount area, and also install a new lock washer before putting the flywheel mount nut on. I use a big strap wrench, or you can use your clutch holding tool, to hold the clutch end of the motor, then install the flywheel over the stator, ensuring it mates properly with the woodruff key, then install the lock washer and flywheel nut. Grip tightly onto your clutch holding apparatus as you torque up the flywheel nut.

Install, loctite and torque the bolts which hold on the recoil cup.

And then install your recoil into place. If you were smart you marked everything before you took it off so you know where everything lines back up during assembly.

Lastly put on the motor mount plate and torque the nuts to spec.

This motor is now ready to put into the chassis. Woo Hoo!!
Sadly I have no pics of the motor installation to the chassis, it was about 2:00 AM, I had a ride planned for the next day at 8:00 AM and had to git r done. But here are a few tips...
First thing to do! Place motor into place in the chassis and bolt it up. Then plug in all the electrical connectors and check for spark. It would suck to have everything together and have to tear it down again because of no spark, eh.
It is pretty much impossible to install the motor with the y-pipe on. So leave it off and install after the motor is in.
The reed blocks have a torque spec, but I have always just run them "snug", as it is very hard to get a torque wrench in there.
For this case mod done by Seadooclinic.com, the oil pump basically needs to be turned up all the way. I am gonna talk to them about this some more, I am running like, 18:1 on my gas oil ratio.
Before the reeds go on, bleed that darned oil pump. Yes it is messy! But, you gotta do it. If you look at the last pic I posted you can see the bleeder screw on the front of the oil pump. Make sure your oil reservoir is full and take that screw out. If you are a sissy, you can stuff some rags in there or something, real men just let it run out the bottom of the sled onto the floor. After you get a solid stream of oil, reinstall the bleeder screw.
Also before installing the reeds, check the boots over very well for delamination and cracks. Bubbles in the rubber is the beginning, it goes south fast after that.
Don't forget to add coolant to the sled before you run it! When you first start your sled let it warm up really well, feel the heat exchangers and make sure they are warm. Lift the front end up higher than the back and run the sled. This helps purge air bubbles out of the coolant system. Top off coolant bottle as needed.
Everyone has their own ideas on break-in. I posted mine in another thread earlier today
HERE.
I am sure there is more, be patient with me, I'll re-read over the next couple days and add things as I remember them.
Thanks for reading and Dootalking with me!
Jerry C