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Andy old chap, give us a clue on what mischief you're up to! If you're doing any sort of major work and there is a hint of doubt, then replace all the engine rubber mounts and check alignment, as per the FSM. Same comment applies to the big twins, which is where my experience comes from.
The company made jigs to create the main cradle and the necessary tubes for it to bolt to the frame at the swing arm points and top shock absorber points. It is a bolt on kit that can be reversed.
When I bolted the cradle on the belt pulley was out of vertical by about 4mm. I took the frame and cradle to their workshop which they reworked to make it square.
I bought the bike used, it is a 2008 bike with 9k on the clock.
You are worrying me now in that if I have to change the rubber mounts it will affect the relationship of the pulleys.
Andy, your bike is essentially two separate entities: the frame, plus the engine. The frame is made to a set geometric 'shape' and if the trike conversion has been added so that it aligns with critical features of the original frame then all will be just fine. The engine is assembled into the frame via rubber mounting points and can be aligned to the frame, once installed. That is all spelled out in the FSM and IMHO shouldn't be any different for your trike. If you change the rubber mounts there should be be no change in the relationship between the pulleys. The Swingarm and hence the rear wheel are mounted off the rear of the engine unit, not the frame, so the pulleys should always be correctly aligned relative to each other. I've had literally decades of experience, with MZ 2-strokes and Harleys, with their respective rubber-mount systems.
I see how the swing arm references with the engine but the trike also uses the suspension fixed point on the frame.
The bit that now worries me is the supplier told me in his opinion the engine wasn't aligned as his setup. If you are saying I can change the rubber mounts but still set the alignment of the engine like it is now then I am golden.
As I am doing pretty much the same procedure on a xl1200v right now you can do measurements between different points. I personally did some self made method with rope as seen here:
If the engine is out of aliment check your engine links (i.e. the 3 pieces of metal with spherical bearings - 2 on the front 1 on the back) two of mine has vertical movements which led to the left rubber mount being lower and tilted the entire engine o the left. Same can happen if they have lateral wobble in which case the engine might twist.
But generally measure the distance between the swing arm points and the engine mounting bolts. Then between the frame (lets say handle bar ataching points) and the end of it and finally between the frame and swing arm/engine mounting points that should give you an idea in which direction the engine/frame are displaced with respect to each other.
Andy, we can better understand your query now, so thanks for those two photos. Your rear sub-frame is mounted to the bike frame and the rear-wheels drive is mounted on the sub-frame, unlike the solo installation. Assuming the sub-frame was jig-built (I can't see it being made any other way), then the relationship between front and rear pulleys can only be readily adjusted via the engine mounts IMHO. The lower front mounts for the sub-frame appear to be spherical bearings, which helps with alignment during assembly. The top mounts look darned solid, so nothing is going to move there!
Now you've got our interest, we look forward to further photos and reports on your progress!
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