It sounds that you have done this job differently than I have been doing, so you would need advice what to do next from someone who has done as you have. FYI - I have several sets of headless stock maker screws that I turn into the receiver snuggly - then wrap aluminum foil tape around the screw shank so it just barely slides in and out of the wood stock hole - that way the thickness of the tape is going to keep the axis of the screw in dead centre of the hole - that tape usually prevents any epoxy from going into that hole either - needs release agent all over, though. I suspect that you need to know that your action screws are in the centre of their holes through the stock - not touching when tightened up. If you have threads in the epoxy - must have been formed or cut by the action screws - so would be too small hole, I would think?? But I do not really know that.
If it helps - I often have made short "tubes" to go around the rear screw for Mauser - to hold the receiver and rear end of trigger guard apart - so is usually a 1/4" diameter action screw - I use a 5/16" drill to ream out the little "pipes" and then use that aluminum tape on the bedding screws so that I believe the 1/4" diameter action screws end up dead centre within a 5/16" diameter hole.