EDITED

the total is .003 as you are +.003 to the L and +.002 to the R

Which means the R is .001 closer to the center.

You did make sure your indicator was preloaded before zeroing it and starting your measurements RIGHT?
By preloading I mean that the stem of the indicator was pushed in .100" or so (usually) and then the dial (face) was rotated till the Zero lined up with the needle. This assumes you are using a 0 - 1 inch indicator

The reason I ask is because you cannot be + in both directions on the same plane (9 o'clock and 3 o'clock) unless the opening in the bell housing is not perfectly round. It's not a bad idea to run a little 80 grit around the inside of the opening BY HAND to knock any burrs , excess paint etc. off

If your indicator was preloaded and the indicator mount was solid, put it in and move on

To try and explain a bit further using your drawing as a clock, You are furthest out at 9, (+.003), at 12 you are (+.002) which is closer to the centerline. But at 3 you are (+.002) which is not possible in the same plane unless as mentioned
1. The indicator was not preloaded
2. The indicator mount was not solid and steady
3. There is a burr or other irregularity on the ID of the bellhousing.

You can deburr the ID and retake the readings making sure the indicator is preloaded
OR roll the dice and run it
Your call, keep us posted