You're not alone, lol. I had the same issue and found out that when transmissions are rebuilt all the parts aren't replaced. The first thing I'd check would be your shift cylinders, there are 4 of them all grouped together on the driver's side of the transmission. Standing on the driver's side of the vehicle (right behind the tire) there is a cap on the top left hand side of the transmission but it looks like the sidewall of the engine. Pop out the 4 bolts give it a tap and the cap will pop right off and you'll see all 4 of the solenoids. You can also check the pressure switches but I doubt any of those won't make your car limp.
Did the car go into limp mode immediately after the rebuilt transmission was installed, or did it work properly for a while?
This is definitely a case where having a laptop with HDS (Honda Diagnostic Systems) installed, and the prerequisite adapter would be crucial. With it, you can drill down into the inner workings of the transmission and get an idea of what's really happening. Without that (or at least doing a regular OBD scanner scan), you're shooting in the pitch dark.
Thank you for the feedback, as for the Transmission it ran great for roughly like 9 months and then from one day to the next it went into limp mode.
I will try and clean the shift cylinder and go from there. I been hesitant in taking It to the Acura dealer but if the shift cylinder cleaning does not work that will be my next step.
Thank you again for the feedback.
Here is a diagram of most of the external items that could be affecting your shifting.
I'd really suggest getting some sort of "deeper diagnosis" with a Honda HDS-equipped laptop, or maybe a full-feature Honda-specific scanner (Foxwell? I don't have experience with any of those for the Honda, but like the ~$100 Autophix unit for my BMW). That may well show some errors that will point you to the specific problem, saving a lot of time and money.
Habby is right about trying for a deeper diagnosis, good luck finding someone with an Acura specific scanner though. There's not an Acura dealership within 3 hours of me and the Honda dealership looked at me like I was speaking Swahilis when I asked if they had the capability to scan it (other than reading the codes). I'm just not in a position to get rid of the damn thing otherwise I definitely would. For what it's worth from what I've come across there does seem to be a trend of having transmission issues post rebuild with MDXs, I haven't come across any real reason as to why though