Went ahead and saw my mechanic. After seen the pics, he said that the seal is probably broken and will need a new one.
He also mentioned that the transmission bearing could be broken might , i'd need a new transmission. Only way to check it is to remove the axle.
Also since the transmission mount is weak. That will need replacement as well.
I went to transmission shop. They test drove the car. I explained to them the clunking/ jerk problem.
He said, the seal wouldn't cause the jerk but would cause my engine to act up unless i top it up.
He said the transmission mount will cause some vibration and the jerk will happen constantly but not my shifting.
He thinks the transmission valve are probably too 'sticky' in the morning. This is why i'm experiencing the jerk and the symptoms subsides after i drive the car for few mins.
This will be even worst in the winter.
Now i have 2 options.
Either i go ahead and do a full engine swap, possibly a jdm f23A engine and transmission. Those are running between $700 and $1000.
2. I fix the seal and the transmission mount and see what happens but i will pay for labor.
Get that axle seal replaced asap..Same as i originally suspected curse of the autos, hard shifts in the morning till you ride it off, best bet is to let it warm up beforehand maybe 5 minutes just to get the valves lubed and working efficiently..the low fluid from the axle leaking would definately cause jerking etc if the tranny gets low and the oil gets overworked..idk about the "engine acting up" he mentioned but i do know that from experience you let it warm up or it will be jumpy/jerky and shift harder because its still cold
with a bad mount you can feel it in the steering wheel its pretty evident if its bad, my steering wheel is dead still when my engine runs i can barely feel any vibration
and depends how much you wanna pay right now, my rule of thumb is "quickest and cheapest first" something simple can be a easy fix before swapping the entire engine/tranny imagine labor on that swap compared to an axle seal and top off+mount