So i have an 89 5.8 f150 i recently heard a strange knock coming from what sounded like the bottom of my engine and well i yanked out the motor through it on a stand and while looking at the crank and all the pistons nothing seems to be out of order im a new mechanic so could the knock be something small enough to elude they eye like mabey a crank or connecting rod bearing

 

A deep sounding knock or thumping is usually a bearing. It will have worn to the point that it can't hold pressure to build up that film that keeps the bearing from touching the crank (a couple thousands of an inch clearance).
It doesn't take long after that for the crank to wear the bearing to the point that it can move a bit on the crank and then it starts banging every time it goes up and down.
Grab your connecting rod caps one at a time and start shaking them. One may be a lot looser than the rest. It'll be obvious when you pull the cap and look at the bearing.

 

They all jiggle a little it doesnt seem one jiggles more than any of the others could they just all be worn be cause the knock wasnt really loud i almost thoughy lifter but i was positive the noise was comeing from the bottom of the engine

 

And when it comes to the parts i have if it is just rod bearings should i return new connecting rods and should i use or return the new crank shaft

 

since you already have the motor out, the first thing i would check on the 5.8 is the number two main bearing. the last two 352w engines i have inspected the number two main bearing was not only spun on both engines, but completely toasted on one engine to the point of pretty severe main cap damage.

after that i would pull a few rod bearing caps and check them out, its possible that you have a bad rod bearing and have it feel like normal. the only way to know for sure is to check the bearing clearances.

 

Ok so i have removed all rods and checked bearings the seem to look in good condition no scuffing accept a tiny bit on cylinder number 8 i beleive and have now removed the crank shaft and all those bearings appear to look fine aswell accept a bit of darker color and some light scoring on the bearing closest to the rear seal could it be damged but not be visible just by looking. How would i check the clearences

 

sounds good, you can check clearances with a product called plastigauge. you just cut little strips, and then torque the caps down, then remove them, DO NOT turn the crank otherwise you ruin the measurement and have to do it over again. then using the strip of paper the plastigauge comes in, you measure the width of the now compressed plastigauge. once done remove the plastigauge.

you can also check the piston to wall clearance by using a long feeler gauge.