[kevbo22]

To day I ran a indicator in the spindle, it was fine.. maybe 2 tenths out.
I put in the r8 and the haimer tool holder and ran the indicator in the tool holder bore. a thou of runout.
I ordered another tool holder from tomach last week, but it still hasnt come in the mail. I leave the country for work on friday morning for 2 weeks. I think im going to have to start back at it after I get back.

I would do the following:

1. Remove the R8 collet and indicate the spindle taper to see how true this runs.
2. Check that the R8 alignment pin inside the spindle is not sticking into the spindle too far. I had this once and it would impinge on the collet when tightened and cause runout.
3. Insert the R8 collet and a 3/4" ground rod or a long 3/4 dowel rod. The rod/dowel must be straight. You want some stick out so you can check runout close to the collet face and also a bit away from the collet.

As far a using a V block to indicate the probe tip in, that will get the probe tip concentric with the TTS shank, but if there is runout in the spindle taper or the R8 collet then the probe tip will not run true. The goal should be to get the tip to run true to the spindle bearings, so a V block isn't the correct choice in my opinion. I would do as you have been doing and make a clocking mark so that the probe can be inserted the same way each time.

"Check that the R8 alignment pin inside the spindle is not sticking into the spindle too far." ---How far is to far?

I have some precision ground drill rod, but I know its not straight. So should I use a gauge pin? Or would that be too short?