The first thing you have to keep in mind is that when you just start seriously lifting you are going to find significant gains right away no matter the program, and you are going to have some slowdown in your gains after the "honeymoon" stage is over. When you have more to gain, you will gain more. It is the same in fat loss, when you have more to lose you will lose it faster. But that slowdown shouldn't come to a plateau.
I was a football player for 16 years, including 4 at PLU and I started heavy olympic lifting in sixth grade, with over a decade of experience now. I have encountered numerous plateaus as well as numerous extremely long periods of steady, albeit gradual, gains. What I have seen over and over again is if you are hitting plateaus, but steadily lifting, it is almost always the program to blame, not the little extras you do on tuesdays/thursdays. I would always recommend doing little extras on "off-days," so long as the little extras are low weight, non-failure exercises.
It is fairly well known that when you lift heavy you are causing micro tears in the muscle fibers, mostly to blame for soreness. These micro tears are healed during rest periods, mostly sleep, and the muscle comes back stronger than before.
When your body runs out of stored ATP (anaerobic energy source) it produces lactate (lactic acid) in the muscles to help with the synthesization of glucose, which is involved in the creation of energy, with the purpose of extending your exercise. This lactic acid is the source of the "burn" you feel towards the end of a hard lift. The pain is actually a defense mechanism intended to cause you to stop the hard anaerobic exercise before you cause permanent damage to your muscles. (1 a lactic acid explination) And in the rest period between lifts the creatin stored in your muscles take the responsibility of creating more ATP to use the next time you demand anaerobic exercise from that muscle group (2 a creatine simple explination) (3 a creatine study).
What causes you to feel "stiff" the day after a hard lift is not due to soreness, or to the tears in general. It is caused by the pooling of lactic acid in those new tears. The lactic acid that was created during the initial lift, unless explicitly worked out, will pool and sit in the newly opened "pockets" that are the micro tears. This pooling of lactic acid is actually a hindrance to your muscular recover. The side effect is essentially the same as that of swelling in a newly injured body part, the reason for the RICE mnemonic (Rest Ice Compression Elevation) you are supposed to follow immediately following an injury; to reduce the swelling and get the pooling fluid out of the injured area (4 RICE explination). The micro tears are a minor injury to the muscle fibers that the body needs to heal. A pooling of fluid in the injured area is going hinder the flow of fresh blood to the injured area, causing a slower rate of recovery.
So doing these little extras on tuesday/thursday is actually beneficial to your muscular recovery because it is causing an increase in your blood flow and helping to flush out the pooling lactic acid from your sore muscles. This is only the case if the exercises you are doing are infact light weight. Lifting to failure in the same muscle groups 2 or more days in a row may in fact limit your ability to properly recover. What I would recommend is that you add foam rolling to your daily routine.
From what I can tell about the Stronglifts 5X5 is that you do mostly 5 sets of 5 on your lifts for most of the time. This is going to cause plateau's because you are not "shocking" or "confusing" your muscles (5 a great offline paper source) (6 a simple explination of the principle) (7 some easy to follow guidlines). Doing the same number of sets and reps daily or even weekly is not going to cause continual gains, you will hit a plateau as your body is continually trying to reach a point of homeostasis. This I have seen over and over in my own experience. The great programs I did where I saw gradual but continual gain in every area were the ones that switched up components of the routine every week. I have never seen any real benefit come from doing the same number of sets/reps every week. You can not expect continual gains to come from the execution of the same routine week in and week out.
I am sure I will receive flack for that statement because there are a lot of people out there with "proven results" for their specific workout routines but what I can tell you is that I have never gotten a workout routine from a website that promises results. All of the programs I have been on the past 11 years have been created by athletic training experts in the fields of Kinesiology, Personal Training and Sports Medicine, designed for maximum continual gains. There is no such thing as a sustainable "Get Ripped Quick" program. And any program that promises "You'll add 100 pounds to your lifts every month...." like the StrongLifts 5X5 program, is a lie. It isn't sustainable, and is not possible to make a claim that someone is going to gain an arbitrary amount of strength.
If you are looking to get stronger and more athletic without a plateau I would suggest finding a college's sports training routine because they are going to have the most research and science behind them, with the least amount of flair and promises. Here is a guideline from the University of Florida made for it's football program which gives a good explination of how a proper fitness/lifting program should be outlined.
If you are serious about wanting to be fit and strong, which it appears that you are considering the 5 days a week in the gym and 2 days a week of martial arts, which is awesome by the way, then it isn't a matter of just following a set routine and there you go. It is a lifestyle of fitness and nutrition that you adopt and live. Not a workout program that gets you ripped and strong in a matter of weeks.