Big hugs to you Britt!!! From 3-4 mos is a pretty major transition time for your lo, so hang in there! First, some of the nap issues are developmental. Babies organize night sleep first (0-3 mos) and day sleep later (3-6 mos), so some of it will work out over time. That said, there are a few things you can try.
Most 3 mos olds can handle 1 hr 20-1 hr 30, but some can go longer. By 4 mos, many los can go 2 hrs. Generally, a 45 min nap would indicate that your lo is ready for longer A time. However, if he's crying for 30 min before hand, that may not be the case. Have you tried starting your winddown routine a bit earlier or later to see if that makes a difference? If he's up at 6, maybe start his wind down around 7:15 (instead of 7) or even 7:30. Is your wind down basically the rocking/shhing? Is he swaddled? That last 15 - 30 min of A time should be really low key - and he may be quite fussy - so just walking around the house, cuddling, etc. then start the wind down.
With our dd, we would go into her room, diaper change, close the blinds, swaddle, sit in the chair and rock, then start shh/pat on our shoulder, and put her in the crib when she was still awake and continue the shh/pat til she was asleep. If she woke early, we'd try more shh/pat to get her back to sleep (but I'd only try for 30 min), then I'd get her up , feed her if she seemed hungry, then basically a diaper change and right back to bed.
So if your ds's first nap is short, try shortening the rest of his A times - so it's basically just eat and back to bed. That OT really can build over the course of the day (as you are discovering). Then for the last nap of the day, if he's not napped well all day - just do what you can to get him to nap so you don't have a super OT baby for bedtime. Preserving that night sleep will help you (and ds) make it through the next day!
Hang in there! It will get better. You may want to check out the EASY FAQ on transitioning to 3.5 or 4 hr EASY, as he may be in the early stages of heading that direction.
HTH
michelle