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Just put a new sink in and was not lucky enough to have the plumbing line up. I have it roughed in and wanted some insight/opinions on whether this will work, or what I need to do to fix it. I have a slope leading from the disposal to the trap, but with the new larger sink, my p-trap is about 2" lower than it previously was. I used a J-bend to meet the drain tail piece to the drain tube. It seems like I am fighting gravity a bit too much now as the distance between the p-trap and the drain tube is quite large. Will this setup work or do I need to approach it a different way?

You DO realize you can (perhaps even "are supposed to") cut excess length from the slip-fit trap parts? They are supplied long, but don't need to STAY that way. You can cut most of the tube leading to the trap off, thus raising the trap.

Opioninated commentary: I'd also lose the "flex section" on the other side of the trap - it is the part of this setup that will break first, by a long shot, in most cases. Also helps to promote clogs before then. You should be able to line rigid parts up by rotating them. In this case looks like you might also need to trim the "J tube" slip-fit end to make them line up right.

The flange piece connected to the sink looks like it isn't mounted flush and could cause leaks. Readjusting the garbage disposal might fix that. It also looks like you have enough room to get rid of that adjustable trap and install a regular one. The "jog" in that trap and the excessive length will probably cause water to rise into that sink when you run the disposal.... Good luck.

In the OP's installation the last horizontal run going into the vertical drain appears to be slightly higher than the horizontal run coming from the disposer. I think this will cause the horizontal disposer run to retain liquid. It appears that some of any liquid waste going into the left sink drain would flow back into the disposer. It seems to me that the T in the final drain must be lower by 2 or 3 inches.

See how it is done here (https://terrylove.com/forums/index.php?attachments/kitchen-sinks-jpg.15470/):

In the OP's installation the tailpiece from the sink appears to be out of alignment (at a slight angle) with the next piece below it. But this may be an illusion since it also appears to be the case in the installation shown above.

Bring your Ptrap up or your Sanitary Tee down.

AS noted by others you can cut the tail of the piece where it goes into the top of the Ptrap shorter ( thereby bringing the Ptrap up ), This will allow you to have the down hill slope you need for the disposal. You may need a longer tail piece from the bell on the basin into the tee from the disposal.

OR

I think this is the better option because your san tea is a little to high.

You could cut your drain pipe shorter so the sanitary tee is lower.

Use a regular Ptrap ( non flexible, there is no need for the debris catching flex connection here ).

You also need to mount your air admittance valve properly. It is not high enough, put it as high up as you can in the space between the bowl and the back of the cabinet.

If you put it on a threaded connection just above the san tee you will be able to pull it out to change it if necessary.