Hi Ross, a link or two short in the chain length concerns me a little...the original chain would have stretched over time...but to two links...I don't think so... wink

I'm at a loss here, I haven't had to purchase new chains for my machine as yet...so I don't know the "correct" length for the primary... frown

However, here is a possible solution, just purchase another 'removable link' and place it in the chain and see if that relieves the problem...it may if the chain you purchased was a link short...I honestly doubt if the shaft is bent....the engineer would have seen that prob as soon as the lathe started spinning the reel...it would have been undulating around its own axis...
There should be around 1/2" (12.5mm) play in the chain when correctly adjusted...
It will cause wear on the sprockets and the new chain if incorrectly adjusted. wink
Please keep your eyes on it....and let us know how you get on, Ross,
cheers2

Please do not PM me asking for support. Please post your questions in the appropriate forums, as the replies it may receive may help all members, not just the individual member.
Kindest Regards, Darryl grin