If my tefillin are Nusach Ari, and I'm Ashkenazi, can I re-tie the knots and make the tefillin look Ashkenazi? (Such as re-tying the Shel Yad knot to have the loop closer to you, and re-tying the Shel Rosh knot into a Double-Daled.) Would this prove to be troublesome since Arizal letters on the parchments differ from Ashkenazi style of lettering?
You can always retie the knots but the result won't be the same as Nusach Ashkenaz tefilin.
Many years ago I purchased Nusach Ari tefilin, after being told that ktav Ari was accepted by both Ashkenazim (Litaim) and Hassidim. Once I learned hilchot tfilin in more depth I discovered that there were other important differences between Ari and Ashkenazi tefilin.
Specifically there are different opinions and customs on how to make the spacing between the parshiyos of the tefillin, in particular the paragraph spacing between the last two parshiyot of "Shema" and "Vehaya Im Shemoa" (called the "Hefsek Parshas Stumah"). Many Ashkenazim follow the ruling of the Taz in that respect while e.g., Chabad Hassidim often follow the Shulchan Aruch Harav / Admur Hazaken. According to a number of opinions the spacing of Shulchan Aruch Harav is not ideal for Ashkenazim. The same is true between ashkenazim and sfardim incidentally.
Therefore many Nusach Ari tfilin, even if you retie the knots, will have the "wrong" paragraph spacing for an ashkenazi.
I specifically asked R Yitzchak Berkovits (a respected rosh kollel and posek in Jerusalem) who ruled that tfilin nusach Ari were fine b'dieved (after the fact) for an Ashkenazi but not ideal because of al Titosh Torat Imecha (do not forsake the Torah [teachings] of your mother -- Mishlei/Proverbs 1:8).
The fact that there are different opinions on how to make the Hefsek Parsha Stumah in tefillin is less known and far more serious than people realize. Ignorance in this subject can cause a person to purchase a pair of tefillin that are not correct for his particular custom. Furthemore, incorrect paragraph spacing may even render the tefillin possul, for certain people, as explained below. Unfortunately many vendors of tefillin are themselves either ignorant of or indifferent to the different opinions and customs of Hefsek Parshas Stuma. Sometimes the discrepancy will not be picked up for many years and will only be brought to the owners attention much later during a routine tefillin examination.
Because of this it would be better not to try and switch tfilin from one nusach to another. As always CYLOR for a practical ruling in your case.