so after installing the pass u-joint and tried to grease the unit before installing the axle back in the truck and it seems the grease will not go in, am I doing something wrong with the fitting and the adapter I had to get for my grease gun...

ALso after I greased the lower ball joint, should I install the cap plug as it looks like the will not be any clearance with the front axle. SO to service the lower ball joint do you seriously need to uninstall the front end down to the axle just to grease the lower ball joint,.,,,

 

Lower joint should have had a 90 degree fitting on it. If you are careful, you can change it without having to disassemble the entire axle.

Is it the joint that won't take grease, or one of your adapters that is causing the issue? If the gun worked on its own, without the adapter, I would be looking real hard at the adapter.

 

Your u joints should have come with plugs that go in the holes. You need to remove the plugs and install the 90* zerk fittings. After you are done greasing them you need to put the plug back in. You can NOT leave the 90* fitting in or the axle shaft will break it off when it turns. This site won't let me post a pic location so here is the link.
http://www.turbodieselregister.com/t...aft-by-u-joint

 

Im pretty sure even a 90 degree fitting doesn't clear the axle as stated above. So ya, you likely need to grease it and plug it, no other way really, and the oe ones aren't greaseable so they didn't need to make clearance there.
As far as the U-joint goes, I'd try a different grease fitting.