Can you give a specific example of the handwork you would like to estimate? If you are hand collating sheets how does it work for you to base on number of sheets collated? If shrink wrap, number of sets? If hand marrying pre-collated signatures, separate the machine collating from the hand work and base the hand work on number precollated groups handled?
If you are doing some unusual hand assembly, you should consider doing some "mock production" to simulate the work so you can time it and estimate it.
Bruce Moore
PowerQuote Print Estimating Software