Thank you to both of the replies so far its confirmed a few things, and given me a few things to ponder.

The PK is Non-clustered on the #Lookup table, and looking at the table there is no clustered Index at all, unfortunately id assumed the PK (or secondary index) was clustered, which probably explains the table scan. Id like to see what happens if you make the PK clustered.

I did some 'off-record' testing by dropping the SysId from the joins inthe actual query, and over a couple of runs there was an approx 5% performance improvement.

Also in the actual query the #Lookup table is referenced around 8 times. At the moment the query returns around 25% of the data in a little over 13-14 minutes.