The heads do breathe, but the ports utilize velocity instead of max airflow. The valvetrain isnt nearly as limiting as the stock cast rods and the high velocity ports. RPM isnt needed since the 350 share the same 3.75" stroke as the 400. The main difference, if not the only difference, between a 400 and 350 is the bore size, and the 350 cant be bored to a 400. Just not enough meat there. Everything on the 350 except the pistons and rings can be used in a 400 if the crank is rebalanced for the 400 pistons.
Since you have an intake, I will assume its a Performer, and headers, then all you really need is a cam and some valve springs. If your heads dont have the end bolt holes like Cobalt mentioned, then there are two ways around that. One is the brackets he mentioned, the other is a set of Ram Air manifolds for D ports. They run about $300 but will seal without the end holes, and not cost you lots of power like the log manifolds.
http://www.ramairrestoration.com/catalog/index.php?cPath=31_2_21
Here are some inexpensive cams that work quite well. Despite what people say, Pontiac engines dont have to be super expensive to build, and often can be done cheaper than a power comparable chevy.
This cam would work well, have a nice idle, and make good power.
http://www.summitracing.com/parts/SUM-K2801/
This one works good in 400s and 455s, and is a bit rowdy for a 350 but not terrible.
http://www.summitracing.com/parts/SUM-K2802/
These two are ok in a 350, and shouldnt cause a loss of low rpm torque. With ported heads any of these cams would work even better.
http://www.summitracing.com/parts/CCA-CL51-232-3/
http://www.summitracing.com/parts/CCA-CL51-222-4/
The other thing you could do if you have an automatic is swapping in a mild stall. Any transmission shop will have what they call a Th400 high stall converter. Its a full size 13" converter with a stall speed between 1900 and 2200 depending on the engine and vehicle. Alternatively you could swap in an off the shelf 2200 or 2400 stall, they dont slip that much and will give you just a bit off the line without wasting lots of RPM. Those converters will fit either a Th350 or a Th400, so if you have one of those its an easy swap. Any gear it has now, as long as it isnt 2.41 or 2.56 will work, but there really isnt any need to go deeper than a 3.42/3.55, and that will mostly raise the highway cruise RPM. I like a 3.08 behind my Pontiacs, and also the 2.73 works well provided you dont cam the engine to have a hole at the bottom of the RPM range. You have more torque to start out than a chevy does, so you dont want to build it like a chevy, if you do it will be a slug.
If you find a 400 or 455 block later you can swap most of the stuff you have in your 350 to it. Those cams in a 455 would be a stump pulling highway cruiser that shreds tires for fun.