[godruler]

what exactly is happening when you say it all the sudden stops bleeding correctly?? does fluid come out smooth? intermittently? no fluid coming out at all? do you have a vacuum bleeder, they are helpful sometimes if you have a very stubborn air bubble.
Did you grease your caliper slides real nice?? on a few occasions i've seen honda's that had weak pedal pressure be caused by sticking caliper slides because of the increased effort to push the piston out when the caliper freezes on the slides.

also when did this problem come about? was it prexisting before you started doing all this brake work or no?

deteriorating rubber brake hoses can also cause a clog in the line, considering you replaced pretty much everything else i'd get some because they are cheap insurance and then bleed it all again.

 

[godruler]

i'd have to say replace the lines definately, even if it does'nt answer your problem its a good idea anyway. I replaced mine when i bought my Crx a year and a half ago and i remember they were pretty cheap. Like Jfro said though stainless is'nt a bad option either, i recently just bought a full set of Goodridge Stainless lines off honda-tech for like $110 shipped. I did'nt install them yet though because i head rumors that they were out very fast when exposed to dust and dirt so i'm trying to find some heat shrink wrapping to cover them all with.