If the pops and slings work in ball search and/or test it is probably a switch issue. Start on the simple stuff before you jump to board level repairs. Go into test and select switch edge. manually trigger every switch in the game, write down any switch that does not register, and we can go from there.

We're not quite at board stuff yet. First we need to look at the return of the switch column. First unplug connectors 207 and 209 from the MPU board. Since we are looking at only one column this will not take as long to trouble shoot.
You will need an alligator clip. In switch test starting off on J207-6 (clip your alligator to it) touch each pin on J209-1-9
You should hear a bong and the screen should show what switch "closed" for example 207-6 to 209-1 should register upper jet bumper. Write down what switches do not register. After that start with the first switch in the column that doesn't register and check for a shorted diode, loose wire, or cold solder on each switch.
If none of them register we are beginning to move into possible board problems.

Ok, I am a little concerned that you have two columns out on your DMD. Please take some pictures of the MPU board, I'd like to see the bottom 1/4 of it, as close as you can possibly get to the board. Make sure you have all the connectors, the U20 chip, the battery holder.

Also please let me know if you had time to test the column like I described in my last post.

Oops, the missing columns are completely normal, I was not paying attention to those columns when I was looking at the matrix chart. If you already took the pics go ahead and post them anyway. But definitely test each of the pins in the rows and columns as described.

OK, looks like you may have a blown U20 chip, or a broken trace from the header pin to the U20 chip. Take your meter and set it to continuity, put the black lead on J207 pin 6, then put the red lead on pin 13 (should be the fifth pin from the left on the bottom of the chip) of U20. If you get a tone the traces should be fine.
Power off the machine, reconnect the J209 and 207 connectors. Then power up the game, go back into test and see if you are getting any voltage from pin 13 on U20
After that, with out a logic probe, switch to DC voltage on your meter, black lead on ground, red lead on pin 13, on a working chip you should see 12Vdc coming out of U20. If there is no voltage, I'm pretty sure that chip is dead. Hopefully, it is socketed and you can pull it and replace it with out desoldering the chip from the board. If it is not socketed, and you have never desoldered an IC from a circuit board, send it to someone to repair, and have them socket it for you.

Without battery acid damage, there must have been some coil voltage that ran up the switch matrix to fry that chip. After you replace the chip and before you power up the game go over every switch in the row again to make sure that there isn't anything (a loose wire, diode, screw, lamp base, etc.) touching a coil or you will blow the new chip again.

Yeah, lightning is pretty bad for most of your electronics. It might help to have your pins on a beefy surge protector in the future.

As for a new chip, ksarcade.net may have them, marcospec.com usually has them, along with actionpinball.com and I think pinballlife.com.

Let us know when you are back up and running.

Excellent. Make sure you mark the thread as resolved, and enjoy your game.