Gonna preface this with I have no experience :P But I'll take a stab at it anyway.snip
Only thing I'm not sure of is your last step. You say you put in your time from the RNGR into the Eon Timer + 90 frames for an offset, but are you taking into account the time since you started the game? From this post it sounds like the frame at which you get the Dratini is ~500, which is similar to the offset you're seeing. Could be a coincidence, but that could be your issue. It looks like that download link to Misdreavus' timer works still if you're interested in trying it out.