There is nothing user friendly on any of the new high efficiency boilers. They are not designed for the home owner to work on period. If you want to work on your unit I suggest you study the factory manual for your unit and then back that up with about 3000.00 worth of special tools and a class in boilers. I am not meaning to sound cruel here but just stating the facts.
Peerless gave me a preproduction unit 5 or 6 years ago so we could play with it at the university and play with it we did. Over a short period of time we replaced most of the control parts and removed the exploded fan assembly parts from the combustion chamber. From what you are saying they did not make any improvements to the unit even after we gave them all the feedback.
The biggest problem is the install for the most part. Just because a unit starts and run does not mean it is working correctly. These units are not setup to work correctly right out of the box they need to be adjusted/fine tuned since every install is different. Most of the ones I have seen in the field are not even running in the energy saving mode (condensing) since they are replacement units and the system was not designed for such a low water temperature. If you do not run a constant 130-135 degree or lower return water temp you are not condensing and not saving that much gas so the savings theory goes right out the window.
This is just not a Peerless problem but manufactures almost across the board are having problems. There are just not enough trained service techs out in the field to set them up and repair them properly. On another note all these units need to be serviced/cleaned by a trained tech EVERY year so if you cannot find one to do a correct install you will never find one for service.
So far I have not given you any insight that would help and what I am about to tell you will probably not make you happy.
Find a trained service person and pay them to take care of the problem child OR replace it with an 80-87% efficiency standard design boiler and chalk it up to experience. It might cost you but the problem goes away and the old style unit will last 25 years or more and be trouble free for the most part.
Peerless is a good company who like all the rest jumped out to claim a portion of the high efficiency market. As usual these boilers were sold by a supplier to dealers who did not know exactly what to do with them and this is the result because if the dealers actually new how to install and work on them there would be no problem.
The funniest stories come from home owners who buy one off Ebay. They have no idea what they have but try to install it since many home owners feel they know it all to start with. Then the boiler companies start to get all kinds of phone calls asking all kinds of stupid questions. This is part of the reason they did not want to talk to you on the phone since it is very hard to deal with people who do not have any idea what they are doing and all the questions should be directed to the dealer who you contracted with to do the install etc.
It costs a manufactures a small fortune to keep sending parts to someone who has no idea what they are doing. I guess the mentality is you just replace every part in the unit and eventually it will work. This is wrong. NO part ever needs to be replaced until it is tested and proven defective. All boiler manufactures have a trouble shoot section in there boiler manual and all you need are the proper tools and the knowledge in how to use them to find the exact part that is causing the problem to start with. No matter how bitter this might taste it is the truth and I would rather state that than do a hand holding contest with no positive outcome. Sorry but without being there to actually test your boiler I can be of no further help except to say I told you the truth.
One parting fact. There are some good boiler men out there. They do a good job of installing and servicing the new style condensing boilers. If the job is qualified to be able to use the new style boilers and the boiler is installed properly any other problem that comes up is usually minor in nature. All the manufactures units being sold today work but only in the hands of an experienced person who has spent many hours in class to study the new style systems and has the proper tools to make the repairs when necessary.
Get your IO/M revision 1 manual here. It is 91 pages long but download it to your computer so you can review just how detailed it is and also find the trouble shooting tips. Most of the trouble shooting is done by the circuit board and announced on the display. Good luck. Peerless® PUREFIRE®