I am having an identical problem on my ford 3400, which has the same rear hydraulics as the ford 3000 as far as i understand. I just replaced the same things you did, even got the suction filter out and got it completely clean, cleaned out the whole rear end etc.
I'll list a few ideas, I've already checked these on mine to no avail but maybe they will help you:
- Draft control knob screwed mostly back in? (You would have had it all the way out if you adjusted cam follower height like me, and it would barely lift deliberately as a result).
- I read to only use the FNH unloader valve o-ring, as that part is sized critically and cannot be replaced with a standard o-ring. I used the correct part though, and still have this problem. The correct o-ring does not come in the standard lift cover o-ring gasket set so it could trip you up. I don't know exactly what the unloader valve does, so I'm not sure if this would even cause this problem though.
I'll keep an eye on this thread, please let me know if you find a solution as it might help me with my problem (i'll do the same for you). Currently my lift takes over 20 seconds to raise.