I emailed the Small Engine Warehouse (where I got the Honda repower kit) and requested a procedure for aligning the engine with the driveshaft but no-one replied to me. Luckily, my neighbour is a milwright and he gave me a hand with the use of his dial-gauge. He strapped the gauge onto the driveshaft adapter (between the pilot bushing assembly and the crankshaft) and measured the deflection of the driveshaft as I rotated the engine.
I was able to get the engine alignment pretty close side-to-side but the dial gauge showed that the front of the engine was too low. Putting a thick washer between the new motor adapter plate and the original engine plate raised the engine just about perfectly. The rear rag joint was a lot less stiff than the new one and had taken a bit of a stretched deformation (like the engine was previously mounted slightly too far forward). I pushed the engine backward to make the rear rag joint look flat. I wanted to ensure that there wasn't any unnecessary sideways loads on the hydrostatic drive pump.
If you need to replace the rag joint on your Honda engine, I would suggest that you replace both the front & rear joints at the same time. I thought I was buying a set because there were 2 disks in the package but realized later that this was only for one joint. I would also suggest that you buy a pair of speed nuts for securing the bolts of the pilot bushing assembly. These don't unscrew very easily and will probably get a bit mangled as you remove them.
[I later called SEW about the engine's alternator rating and got someone from the tech support department who was quite helpful. He said that they may not have replied to my earlier request because my engine was out of warranty. As I was just looking for a procedure, I thought this was a lame excuse. Anyway, they had no procedure to send me. If you need help from the SEW, call - don't email.]
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