I wouldn't worry too much about the layshaft assembly. I had to do similar to get a fraction of end float on mine too.
As to the noise, have you trimmed the rear diff carriers. I'm talking about the mouldings on the diff bearing holder that were originally designed for the XX4 roller bearing. These might be catching to diff pulley?!? Could also be the front bulkhead, have you trimmed it as per the manual?!?
Apart from that, it could just be a dodgy bearing or a bearing that's nipped up tight somewhere. Try disconnecting the driveshafts front and back, then try spinning the transmission again.
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