I tried it again and got a much better result. I used an ER40 collet holder and measured the run-out on the end mill before I cut the hole and could barely see the needle move. It seemed like I was getting less run-out than when I measured with the R8 collet. I ran the cutter at 600 rpm and was pecking and used WD40 to get rid of the chips. The hole is between 0.5 and 1.5 thou oversize. I don't have any gauge pins, so I cannot really measure very accurately. This is definitely close enough for my purposes, though.When using an end mill as a reamer, your RPM is much lower than using it as an endmill. But your feed rate is quite high. Chip load per tooth is substantially more than normal machining operations
Thanks again for your help, Nathan and Callum.