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.
Your question is actually, "Can I change my tefillin into those worn by the Chasam Sofer." Arizal writing. (At least in regards to the tzadi) Square knot. Winding inward. Those are exactly his tefillin.
Inward wrapping Arizal script tefillin aren't unheard of at all.
The modern style of Arizal writing is based on a set of tefillin that belonged to the Vilna Gaon who wrapped inward.
The Gur Hasidis wears inward wrapping tefillin in Arizal script.
Ashkenazi tefillin from many kehillas in Eastern Hungary are written in Arizal script, though with a single daleth rosh, mine included.
Nodah B'Yehuda says you can't disqualify writing that doesn't contradict the Talmud. (Noda B'Yehuda Tinyana Y.D. 171) He and the Chasam Sofer (Chasam Sofer EH 8) say that all present modes of writing Stam are equally holy and valid.
Like Rashi and Rebbenu Taam tefillin are named after the Rishonim most associated with them but represent older traditions those rishonim were referencing rather than creating, Beis Yosef and Arizal scripts likely are the same.
Of the 5 oldest European Torah scrolls we have, the oldest is from Balogna and is written in a style we no longer use at all, 4 are from Erfurt and are written in a style closest to Arizal script. Those 4 are from the 13th century, obviously before Arizal lived.
You can check out the Sheilos and Teshuvos of the Rosh 3:1 for a reference to ksav differing between regions.
Regarding worry over which sections are pesuchos and which are setumah, unless your tefillin were written according to the minhagim of Belz, Bobov, or Chabad - and they weren't unless you specifically asked for that - they will be written with blank space enough for fewer than nine small letters following Shema and blank space for fewer than 9 small letters on the first line of Vahayah im Shamoa.
The is the same version of the opinion of the Taz followed by most Ashkenazim and the default way of writing Ashkenaz tefillin if you don't specify to the sofer something different.
Yes, there are individuals who would be charif, based on the Chazon Ish, but there's testimony he retracted due to the Chasam Sofer using the arizal tzadi in his tefillin (see Minchas Yitchak 4:47) and in any case nobody in real life would say Arizal writing isn't fine bedi eved based on that Chazon Ish.
The only issue you really have is that Chasidic tefillin and Stam Ashkenaz tefillin differ on which word begins which line in the tefillin scrolls.
That difference doesn't disqualify them.