To solve the tool offset issue, it would be easiest to use a common point, like the table. If you have a presetter, you would use the tool gage length as your offset. Thus your tool length would be a positive number. This is a convention used when you have tool measuring probes, or offline presetters and such, and is a reliable means of checking your lengths, as the tool comes into the spindle, before it runs down to the part, you can use a tape measure, or Rule to double check the offset.
If you did this, you could make a dummy tool, as a quazi part probe, and use this to figure out your Z offsets for each work offsets. Take the work offset you measured, and subtract the offset length of your dummy tool!!!!
In some Yasnac Controls this is built in, how you handle your part and tool setup!!!!
"It's only funny until some one get's hurt, and then it's just hilarious!!" Mike Patton - Faith No More Ricochet