Have a good look at your MX5 upright and you will see that it has a twist in it. If you move the tie rod end to the top you are effectively moving the pivot point inwards away from the wheel. If you look on here you will see that some have done this, but in my opinion it is not right. You will also see that some have heated and twisted the steering arm to correct the above and in my opinion this is probably dangerous, although it will correct the problem.
Moving the tie rod to the top of the arm will change the geometry, but I don't think our arms match the original ones anyway. THings will work out OK, if you make things the proper length to match and then check yuour bumpsteer.
I believe that heating and bending the arms is generally considered safe. THe subject has been discussed and people with reasonable experience weighed in.
Have a nice summer, I think you've done a good job on this frame and have something to be proud of! Not to mention something great to look forward too when you make more progress next year. I hope you getting to learn lots of pratical stuff. Plenty of folks never learn all sorts of basic stuff you get to learn when you build from scratch. Plenty more good stuff to do...