Well, it seems that you have been able to rule out the electronics and you state that you feel, what feels like, three gear trying to go in, but it wont.
Given that, I'm wondering if your Forward/Direct drum is cracked. I know the 95 CD4E had a problem with a defective weld, which would cause a crack in the hub and drum. This crack would allow pressure to leak through the Forward clutch packs to the direct clutch packs. Sometimes, you would only see no 3rd gear engagment, other times there would be no forward movement at all.
I know you have 98 and should not have the defective weld there, but your pump could have spiked sometime in the past causeing this crack.
It's going out on a limb, so I will see what else I can find also.
