Newbie with DR125 Weirdness going on?!?

Hi this is my first post on this forum, in the hope that someone might be able to shed some light on the engine rebuild I am doing. Here's the background: bought the bike with no paperwork as a field bike - I think the build year is 1987, it has a disc front and 'full floater' monoshock rear end. Decided to rebuild the engine as the big end sounded like it was shot and do a rebore at the same time. The big end was indeed beyond repair and it was cheaper/easier (ahem...) to replace the crank assembly with a new pattern part which was advertised as for the DR125 e/s. I fitted the crank and it was a good fit, put the cases back together with no problems, fitted the clutch, oil pump, gear selector stuff. Flipped the engine over to fit the stator and flywheel whereupon things started to look odd. Stator slotted straight back in, fitted the woodruff key from the old crank into the slot in the new crank - all good so far. When I mounted the flywheel theough, it didn't seem to slide far enough onto the crank such that the pickup coils wasn't lining up with the flywheel, but worse of all, the cover now fouls on the flywheel itself???

ANybody been there before? Am I missing some painfully obvious thing here?

Any thoughts would be most welcome. I m away working this week but could post up some pics at the weekend.

Thanks for giving this your time

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