John,
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>This sounds very similar to what I would like to acheive.
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>I understand the printing of a production control number and the customer id as barcodes at stage 1. What I don't understand is why do you require the employee's id number be scanned at stage 1 also?

The client wants "every stage" of the process recorded. If it takes too long from step 1 of stage 1 to get to step 1 of stage 2 then there is a problem area. The employee id helps to isolate "all" problem areas.
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>Is it reasonable to print permanent id badges for every employee, along
>machine/operation id bages for every machine on the production floor?

My Time clock app was already set up to use bar codes so all the employees already had bar code ids.

Separate machine/operation "badges" are not necessary. All barcodes (with process description) were printed on a single 8 1/2 x 11 sheet of paper, laminated, and placed at each workstation. I even furnished 2 additional barcodes that represent In and Out to further simplify the scanning.
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>When the employee scans his unique employee id badge, he/she must also bring the the unique machine/operation id badge that he or she is working on to the computer to be scanned?

No. See above.
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>If this method is acceptable, how do I input the production control number that the employee is working on. Must the employee carry a production control barcode also?

This could be a logistical problem in your case, but in mine it is no problem. The paperwork always accompanies the job. You have to have a tracking number that you can scan or type in. Remember, you can still use your keyboard for all input.
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>I would like to compensate for the possibility that an employee may work at more than on job at any given time. Also I would like to consider the possibility that an employee not previously scheduled to work on a particular job may do so unexpectedly, if required by the production manager.

Yes, it's always the unexpected things that make our lives miserable. You can code for the exceptions as they're presented and/or you can use pencil and paper and let the clerical staff input corrections.
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>I would like to make this as effortless as possible without losing any valuable inormation. This will be a new concept for these employees, who most of which have been working without any time keeping for over 28 years, whatsoever.

The best way, in my opinion, is:

As part of our agreement, I follow items through the process as many times that I consider necessary in order that I understand their existing process. While I'm doing this, I talk to employees to get their input, and their concerns about computerization. Many of these employees that have worked at a particular job for a long period of time understand the process better than management and good management will encourage their input.

It usually helps to keep the lines of communication open throughout the development and implementation processes. This works pretty good, for me, as long as all request for changes go through the proper channel.
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>I would like them to welcome this. Also I would like to implement a system which will not have to be revised any time soon.
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>I appreciate your help. It is the first time I would be attempting such an implementation, and your experience is very helpful.
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>Thanks for your help.

I hope this helps.