The starting point, which everyone agrees, is that Benjamin Wolf Spira's father was Yechiel Michel Spira. Benjamin Wolf was born about 1560 and died 12 October 1630 in Prague. Benjamin Wolf was the father of Aaron Simon Spira, who is discussed extensively by numerous sources.
The question is who was Yechiel’s father. There are three primary theories for Yechiel's father Shimon of Posen, Yoseph Yerushalmi Spira, and Nathan ben David Spira.
Lazarus (Neue Beiträge zur Geschichte der FamilieFränkel- Spira. by Ludwig Lazarus) says Yechiel's father was Shimon of Posen. "The “great Gaon” R. Michel, son of Gaon R. Simon, who worked as chief rabbi of Posen in the second half of the 16th century, is considered the progenitor of the highly respected Prague Spira family."
The next theory is that Yechiel was Yechiel son of Yoseph son of Kalonymous Yerushalmi. It appears that the source of this theory is from Mordechai Weitz, who wrote a lengthy article about Aaron Simon Spira, Benjamin’s son. The Weitz article has a lot of information about the ancestry of Aaron Simon Spira. It is detailed, but not sourced. Other books use the Weitz article as a source.
Otto Muneles Entry 172 (page 262) has an entry for Yechiel. This clearly shows Yechiel son of Yoseph son of Kalonymous Yerushalmi. However, the entry does not use the name Spira. The entry for Yechiel’s niece, Rivka daughter of Shlomo also uses the name Yerushalmi rather than Yerushalmi-Spira.
Gal Ad also lists Yechiel son of Yoseph son of Kalonymous Yerushalmi at entry 92. Again, the entry does not use the name Spira.
So, there almost certainly was a Yechiel son of Yoseph son of Kalonymous Yerushalmi in Prague at the time. But it is not clear if that Yechiel was the father of Benjamin Wolf Spira.
Paul Jacobi, The Jacobi Pares Spira tree, says Yechiel's father was Nathan son of David. Jacobi doesn't really have a source for this as he says that Nathan's name comes from his son's epitaph, but there is not (to my knowledge) an epitaph in Prague that says Yechiel ben Nathan. Jacobi's sources for Yechiel all point to his being Benjamin Wolf's father, which no one disputes.
From Page 188 of Vol. 4: 15.2 R. Jechiel-Michel I (b) Nathan II Spira (? Prag 1530-1575 Posen - Cf. Hock Gal-Ed 15 (sub 13); Brann FF 205 (1); JewE XI 522 (sb5)). All three sources point to Jechiel being Benjamin’s father, which is not disputer.
Jacobi cites no sources for Nathan being Yechiel's father or David’s son: 16.2 R. Nathan II (b) David I Spira (With his parents he moved to Prag where indeed he is known merely from his son's epitaph.)
The entry for David is: 17.1 R. David I (b) Schimon Spira (Moved to Prag where he died in 1547; on his epitaph he was praised for his printing and redemption activities. - Hock 379 (87/5052); Bran FF 195 (n.1) & GFS 452 (1)).
Thus we have three respected secondary sources, Lazarus, Weitz, and Jacobi pointing to completely different theories as to who Yechiel's father was. None cite a primary source.
Finally, some additional information that support some thories but not others.
The Jewish encyclopedia says the Cracow Spiras and Prague Spiras were related, but not how. This supports Jacobi's theory.
Podiebrad states that Benjamin Wolf was not in the Yerushalmi Spira branch, but was in the Spira-Ashkenazi branch. But the name he uses most often other than Spira was Wedeles, not Ashkenazi. Podiebrad is compatible with either Lazarus or Jacobi. So if we take Podiebrad as true that does not settle the issue.