Sleepeasy Solution - Nap help

I think I'm at my wits end and really, really hope that someone can help shed some light for me. 

After 7 months of having to wake up 5-12 times a night I finally caved and asked my gfs for help.  I was really against the CIO method, but the combination of lack of sleep resulted in a tense marriage and the fact that my husband is a police officer and has to carry a gun I knew I needed help.  I was told about the Ferber method and the Sleepeasy solution.  I read the Sleepeasy Solution first and felt that it was really for me. I told my husband that I would give it one week and if it didnt' work, we need to do something else.  Well, within 3 days, he was STTN and by day 15, he went down without crying.  It was AWESOME and since then he has been consistently sleeping from 7:45pm-5:30am, waking up for a bottle (he is underweight) and then back to sleep until 7am-ish. 

I couldn't do the nap at the same time because it just broke my heart to hear him cry.  So for the next 4 months, I rocked and held him for his two naps, about 1hr 20 minutes each.  I didn't mind and in all honesty, enjoyed holding my sleeping son and watching TV.  Last month he started fighting his naps in my arms and waking up after 25 minutes so I figured it was finally time to start nap training.

It's been 4 weeks and while things have been a little better, he is still crying when going down.  Not all the time, but most of the time.  And he is only sleeping 15-25 minutes per nap.  He'll wake up and then cry for the next 35-45 minutes.  I have gone through the book a trillion times and it doesn't really discuss what to do when he wakes up from his short naps.  My understanding is that I'm suppose to leave him in there for 1 hour each nap... but it's killing me 'cause he just cries and cries until it's time for me to get him.  I know that naps take longer, but 4 weeks?  I must be doing something wrong?

Oh and regarding check in... what do you do when he cries one minute on and one minute off for 30 minutes?  Do you check in? The book says to leave him if he stops crying for more than 30 seconds since he's learning, but 30 minutes just seems like an awfully long time not to check in.

I've asked my gf who gave me the book and she wasn't really much help since her son never had this problem.  He takes 2 hour naps and wakes up happy.  I've NEVER had DS wake up happy from a nap or even in the morning. I'm thinking about buying other books to see if their nap solution would work better but wanted to hear your experiences (non-Sleepeasy welcome!!).    Thanks in advance!!