As others have mentioned spot facing to achieve a flat surface to reduce deflection is always desirable. However I do not know if you have the option to do that step. I personally was not following everything you had going on. At first I just thought you had a couple of cylinders to drill. Now...
Need more information:
1) Do you have access to a milling machine?
2) What type of cylinder are you working with, please describe it and what do you mean by that the cylinder is fixed?
3) Please describe your "drilling unit". Is it a drill press?
4) If your drill unit can be...
