Point Pleasant, NJ
I agree with @vec-tor, sounds like a switch matrix issue. First, you'll want to grab a copy of the switch matrix chart, which is in the Jungle Lord instruction manual which can be downloaded from ipdb here: https://www.ipdb.org/files/1338/Williams_1981_Jungle_Lord_Operators_Handbook.pdf
You can find more technical documents, schematics, etc free to download for your game at ipdb.org.
Anytime you discover multiple switches aren't working, you want to see if you can find a pattern on the switch matrix chart. Most commonly, you may discover all the switches in a vertical "column" or a horizontal "row" may stop working. There's a couple common reasons for a column or row of switches to stop working. Often, it can be a broken wire that daisy-chains between the switches, or a broken diode at any of the switches on the faulty row or column. It could also be a connector problem somewhere between the playfield and driver board/MPU. Considering you have an aftermarket mpu, we'll assume that it's ok for now...but there are tests that will help us narrow down the source of the issue.
That said, it sounds like you have at least one vertical "column" out on the switch matrix. Here's the switch matrix chart from the instruction manual I linked above:
Screenshot_20211230-102850.png
Note all the drop targets are on 2 vertical columns, column 4+5. The upper and lower eject holes are also on column 5.
To keep it orderly, let's start with column 4. Looking at the top of the chart, you'll see the wire color codes for each column of switches. Looking at column 4, green/yellow is the wire color that you should find on one side of each of the 8 switches listed on that column. The chart also tells us where that daisy-chained green/yellow wire comes from: 2J2-6 (Plug J2, pin 6 on the driver board -- the lower-left board in the backbox).
So, to put this info all together: a green/yellow wire originating from pin 6 of connector J2 of the driver board runs down to the playfield at one of those 8 switches and attaches to one of the switches solder lugs. Another green/yellow wire runs from that same solder lug over to the next switch in the same column, and again and again until all 8 switches are sharing the green/yellow circuit (that's called a "daisy chain"). If you set your meter for continuity/beep test, you should find you have continuity between the green/yellow solder lugs on all the switches, and between the green-yellow lug from all the switches up to the green/yellow wire at the wiring connector 2J2 pin 6. If you don't get continuity between all them, you probably have a broken wire somewhere at one of the 8 switches on that column. In this case, the switches for column 4 include: all 6 lower drop targets, the right kicker/slingshot scoring switch (does the game score 10 points when the right kicker/slingshot above the lower right flipper activates?), and the rollover up at the top left of the upper playfield. The instruction book also shows the locations of each of the switches, it's very helpful since the switches aren't always easy to locate.
Again--you'll note most of the switches have 2 wires--a green/yellow wire coming from the previous switch, and a green/yellow wire headed for the next switch (the daisy-chain). There will only be one green/yellow wire at the end of the daisy-chain. You may find 1 or 2 wires broke off at a switch, and just needs to be reattached. While hunting for a broken wire at any of those switches, you also want to check the diode on each switch. If either leg of the diode on any switch should break off, it can also cause problems for multiple switches on the same row or column. A gentle tug on both legs will reveal if they're broken/loose.
One last thing important thing to note: the daisy-chain of switches at the drop targets may look a little different. Instead of finding a green/yellow wire at each of the column 4 drop target switches, you may see one green/yellow wire at one of the switches and a couple single-color wires used to carry the green/yellow circuit over to the other adjacent switches. On my Black Knight, thin yellow wires were used to carry the daisy chain to the other drop target switches. If you find one or more of those yellow wires broken, you probably found your culprit. Take pics if you find anything questionable and we'll help figure it out. As far as column 5, you can refer to the switch matrix chart for wire colors, which switches to check, etc. Same procedure as you did for column 4, just different wire colors going to different switches.
I hope this wasn't too much info 
--feel free to ask if you need any further clarifications.
