"without the pressure going up" ? pressure can fluctuate but an expansion tank smooths most of it out. you have one, right? if you're getting pressure rise with temp rise, check your tank's condition.
do you remember what the honeywell timer was set at before you replaced it? if you didn't have problems with it before, that would be a good starting point for the new timer.
also, how's your chimney draft? A better draft will keep the fire going longer/better. EFMs won't sit there idling along for days like an axeman but should go longer than 90 minutes. I can get hours on my efm520. Going to an hourly of half-hourly will certainly help. You want the minimum needed to keep the fire going because too much will cause the boiler to get to the high limit and then it won't be able to run if it needs to and the fire can go out. It can be a bit of a balancing act until you get it dialed in...