Thanks Tahoe and Mechie3,
I think I found the answer.
I was really careful to label all the bolts i needed to re-use, but somehow, in the process, I left these unmarked ones on my bench.
I've been racking my brain for weeks about this and it came to me yesterday while on a "run"...... the rear diff!
Sure enough when I go back from my run I grabbed one of the bolts and it fit perfectly on the transmission end of the diff. 4 holes with thread protruding the exact amount.
Problem solved. The one extra bolt is probably a stray from something else.
I have the trans bolts labelled in a ziplok.
Harley