5spd rattle in 3rd gear - ideas?

When driving under normal conditions I hear a light rattling in 3rd - 1993 5.0 5spd - basically stock engine with 112k miles but recent Centerforce Dual Friction clutch - the clutch cable is adjustable down at the fork (threaded rod at the end of the cable - is this an aftermarket design?)and was loose for a while - so much so the throw out bearing was making a loud clacking sound in neutral - it was driven like this for a while - I have tightened the cable and the clacking went away but there are some noises now when driving - Do you think it may be the soft aluminum front bearing retainer worn out due to the un-preloaded throwout bearing for so long??? Throw out bearing? Pilot bearing? Front transmission bearing? (how hard is it to get the front transmission bearing out if it is that?) Thoughts?

I am pulling the engine for a rebuild in the next week and I will see what is going on hopefully. The noise is not too loud - just enough to be heard with the radio off - still shifts great and feels strong etc... it is like a light metallic rattle sound while in 3rd gear driving at normal speed. I am thinking it has to do with the throw out bearing being out of adjustment for so long - hopefully I will find a trashed t/o bearing or pilot bushing - I was wondering how hard is it to pull the front input shaft and change all the bearings related to that - I have a feeling that is where I will find the problem.... I have never worked on a 5spd before - kinda scary - I keep thinking as soon as I get the front bearing retainer off and pull out the input shaft a lot of little bearings will go flying....