What is the meaning of "Lo Nichchad"?
Radak: (It is not denied.) This is like "Lo Nichchad me'Adoni" (Bereishis 47:18). Malbim - one cannot deny that one Maker made both [the body and the Nefesh].
Radak citing Ibn Ezra: [It is hidden from the eye and heart, but] it is not hidden [from You].
What is "Atzmi"?
Radak #1: (It is myself.) It has Kamatz Chataf under the Ayin.
Radak #2: (It is my bones.) It has Patach under the Ayin.
Radak citing Ibn Ezra: It is my Ko'ach (potential). Before formation, there is Ko'ach for old age in a youth, and Ko'ach for speech in a newborn. So before formation, the fetus was b'Ko'ach. This is hidden from the eye, and the 'eye' (understanding) of the heart, but not from You.
Why does it say "Useisi va'Seser"?
Rashi: I was made via Bi'ah (which is done covertly).
Radak: I was made in my mother's womb. Useisi is like "Isu Dadei Besuleihen" (Yechezkel 23:3), i.e. crushing and squeezing. It uses this expression for formation, like it compares him to a piece of milk and congealing it, like one congeals cheese and curdles it overtly. The first drop melts and flows, and afterwards congeals again, like cheese from milk.
Malbim: These tasks were done to me b'Seser, in the part of the spiritual Nefesh 'copied' from hidden Kedushah above. These same tasks were done to the body, which is the Nefesh's garment and the same size as it. It is as if one is the mold for the other. G-dly people said that the Nefesh has 248 spiritual limb and 365 spiritual sinews, i.e. powers corresponding to the limbs and sinews of the body.
Why does it say "Rukamti"?
Radak: Formation of a fetus with sinews, bones, flesh and skin is compared to embroidery, which is in many facets and interwoven.
What is "b'Sachtiyos Aretz"?
Rashi: It is in the lower residence in my mother's womb.
Radak: It is the womb, which is a low, dark place, like underground. Similarly, "Ofan Echad ba'Aretz" (Yechezkel 1:15), i.e. lowly, compared to the Ofanim above it.