If you're not paitent to wait the 15 minutes for the align process, you can click the top right screw on the MSU after you set it to Align and it will "fast align" (sort of a cheat)
Yes, mind that one. Highly recommended.

If it stays at a certain performance index and the green 'nav ready' light doesn't come on, you may have entered the coordinates the wrong way. I think this arises with the FSX display format. People often seem to miss a zero ('0') when entering coordinates due to the way FSX 'displays' them by leaving them out. Stating this because that was my major problem on the first attempts and I often see it happening when folks learn the INS.

When using the double INS setup, both units must get the same input data. This sounds easy, but if you mix up some numbers when clicking too fast, errors likely occur.
If you still receive errors, please post a screenshot where we can see the coordinates from FSX and the ones you've entered in the INS. That helps on judging about the data format, means the missing zero and things.

If all of the above isn't helping, reset the INS by deleting the isd file in the Civa folder. You'll get some fresh units on the next FSX start. Maybe the file got corrupted.