I guess the amm and nitrite readings are due to the move. Some of the inhabitants of the live rock will begin to die off after even a brief exposure to the air, sponges in particular. Disturbing the sand bed could also lead to a small cycle.
When you say 'replaced the filter pad', what sort was it. If it was purely a cotton pad for polishing the water, then yep , that was fine.
Keep up the water changes, you could also add some carbon to the filter, and maybe some purigen or polyfilter to help remove organics.
If you have live rock (as opposed to ocean rock) I would lose the bioballs as they have no way of dealing with nitrates. Do it slowly though, taking a few out at a time (perhaps with each pwc
)to allow the live rock to adapt.
Whats the turnover of the powerheads (lph), adding another can help cycle the rock quicker as it will feed the water past the rock more often. Also, in a 40g tank you prob need a minimum of 20x turnover per hour split between 2 or three powerheads (I used to run tunze nanostreams), so look at around 3600lph as a start. Dot the powerheads around to proveide a varied flow pattern and some surface aggitation.