The clock positions will get you in the ballpark, however, I look for the largest reading and adjust accordingly. If you measure between the 3 and 6 positions you'll likely find the largest deviation, about .100" by my estimation.

The bellhousing is out by .034" in the 12/6 direction and about .035" in the 3/9 direction. Since you have to do all the location change from two dowels, you'll need dowels that will have a total of .050" from what you have now to correct both directions at once. Replace the offset dowels with the regular ones and measure again, paying close attention to both the clock positions and the location of the highest reading. Make sure your dial indicator stand doesn't shift even slightly as you are measuring or you'll end up doing this a few extra times!

I'll be out in your area this weekend if you need a hand with this.