Should I order all items on the Jenoptik quote?

No. Only order items 1-5. Note in addition that pupil relays 1 & 2 are identical (but you need 2), so it's only 4 distinct parts. 

We decided to order items 6-8 from another vendor to save some $$.

After Jenoptik and Thorlabs Gantry, what is the longest lead-time item?

Cambridge Technologies scan mirrors. These can take 3 months, so order them as soon as you can.