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

I found it makes more sense to my pea brain just to subtract 0.002" from all the readings. Looks to me like he's good to go, assuming the caution that TJP has about button preload has been taken into consideration.

please re read previous EDITED post

indicator was mounted to the end of crank by a magnetic base mount and I made sure I had movement of the plunger on both sides of the dial, this all started with a helluva noise when shifting hard into 3rd gear it sounded like you were trying to get it into reverse I pulled tranny and had it checked and all was good in the tranny Darrin asked what bell was on it and it had a Lakewood he said the tolerances are terrible on those so I got a stocker from brewers and installed it and he told me to check the runout the block was also line bored so he figured the runout was off and the noise was the pilot shaft rattling in the pilot bushing I brought him all the parts to check out flywheel, clutch disc and plate, throw out brg and pilot busing, 3500 miles on complete drive train and the pilot bushing was pretty worn and the block was line bored so his thoughts were bell housing runout was out of wack, I've had 5 other manual trans cars and have never encountered this problem
Thanks everybody for the help

I think I understood it both times.

I wanted to be sure the OP did as one cannot have + readings at 9 and 3 o'clock

Uh, but you can. This just means the bell is centered left to right and you don't have the dial zeroed.

Hmm, OK I understand what your saying after thinking about it a minute But if that is the case then the 12 and 6 o'clock readings will be skewed. Correct ?

That is correct. That's why when I see a set of runout readings, regardless of what is being dialed in, I'll always subtract whatever is necessary to get the smallest positive reading to zero. It's the same as resetting the dial, only doing it mathematically.