The first seven weeks of Daniel’s 70 week prophesy

I understand how Daniel’s prophesy of 69 weeks until “Messiah the Prince” has been fulfilled (Daniel 9:25)

Without presuming to read minds, I don't think you do; notice that the vision of Daniel 9 takes place in the first year of Darius (9:1), later identified as the fourth king before Macedon's conquest of Babylon (11:1-4); indeed, Darius II started his reign in 423 BCE, about 7 x 70 = 490 years before the fall of Jerusalem and its temple in AD 70, right in the middle of the Roman-Jewish war (66-73 CE), which lasted for about seven years (9:27).

Of course, one might reasonably object by saying that the text explicitly points to the decree of rebuilding the temple (9:25), issued in the first year of Cyrus (2 Chronicles 36:22-23, Ezra 1:1-2, 5:13-17, 6:3), not Darius; technically true, but please note that Daniel conflates the two historical characters elsewhere (5:30-6:1), where two of Cyrus' deeds (the conquest of Babylon at the age of sixty-two, and the division of his new empire into satrapies) are nominally ascribed to Darius.

Was Jerusalem rebuilt in exactly 49 years (7 weeks) from the decree?

The text you are trying to interpret (9:25-26) places a messiah or anointed one about half a century after the first year of Darius II (423 BCE), which the text conflates with Cyrus II, as shown above; indeed, Darius III, the king mentioned in 11:1-4, whose loss of the empire to Alexander is described in the preceding chapter (Daniel 8), was born around that time (~380 BCE).

• _{en.wikipedia.org/wiki/Daniel_8}
• _{en.wikipedia.org/wiki/Darius_III}

Now, John's gospel (2:20) does mention Herod's architectural endeavors, confirmed by the ancient Jewish historian Josephus Flavius in his books on the Jewish War, to have lasted for 46 years.

• _{en.wikipedia.org/wiki/Second_Temple#Herod's_Temple}
• _{en.wikipedia.org/wiki/Herodian_architecture#Herod's_Temple}
• _{en.wikipedia.org/wiki/Herod_the_Great#Architectural_achievements}

Also, unlike the Synoptics, John places the event at the beginning of Christ's ministry, rather than at its end (Matthew 24, Mark 13, Luke 21). Furthermore, his is the only Gospel to explicitly mention said ministry spanning over three distinct Passovers (2:13-23, 6:4, 11:55-19:14). All in all, the natural interpretation is that there were 46 + 3 = 49 = 7 x 7 years from the beginning of Herod's (re)construction efforts, until the end of Christ's earthly ministry; this seems alluded to elsewhere in the same gospel (8:57).

Of the 49 years of that prophetic period given in Daniel 9, the temple rebuilding was put to a halt for about three years due to legal hassles. Consider, for example, the record of Ezra 4:1-24. Darius made a decree causing the work to stop as they were rebuilding the temple.

In the New Testament, the Jews show how well they remembered the events of those days--for they gave a count of how many years it took to rebuild that temple.

Then said the Jews, Forty and six years was this temple in building, and wilt thou rear it up in three days? (John 2:20, KJV)

Taking the first seven weeks, therefore, as applicable to the period of the temple's rebuilding, we have a clearer picture of why they were marked off from the following 62 weeks of the 69 weeks.

The full prophecy is for 70 weeks. Jesus also reiterated this prophecy.

Jesus saith unto him, I say not unto thee, Until seven times: but, Until seventy times seven. (Matthew 18:22, KJV)

Here again is that prophecy in Daniel.

²⁴ Seventy weeks are determined upon thy people and upon thy holy city, to finish the transgression, and to make an end of sins, and to make reconciliation for iniquity, and to bring in everlasting righteousness, and to seal up the vision and prophecy, and to anoint the most Holy.

²⁵ Know therefore and understand, that from the going forth of the commandment to restore and to build Jerusalem unto the Messiah the Prince shall be seven weeks, and threescore and two weeks: the street shall be built again, and the wall, even in troublous times.

²⁶ And after threescore and two weeks shall Messiah be cut off, but not for himself: and the people of the prince that shall come shall destroy the city and the sanctuary; and the end thereof shall be with a flood, and unto the end of the war desolations are determined.

²⁷ And he shall confirm the covenant with many for one week: and in the midst of the week he shall cause the sacrifice and the oblation to cease, and for the overspreading of abominations he shall make it desolate, even until the consummation, and that determined shall be poured upon the desolate. (Daniel 9:24-27, KJV)

A "time" in Hebrew could also mean a "day" or a "year" (Hebrew word "yowm"). In the Jews' mind, therefore, it was a very small step to understand the connection between 490 "times" or "days" and 490 years. This was something they should have grasped. Jesus was seconding Daniel's 70-weeks' prophecy--and applying it to the times of the Jews' final probation as God's chosen ones.

Back to your question about the first seven weeks--most of it, 46 years per the Jews' recollection to Jesus, was spent rebuilding the temple. The few remaining years of this period comprised the times during which the temple's rebuilding had been stopped due to the determined resistance of the enemies of the Jews of those times such as Sanballat, Tobiah, and Geshem who wrote certified letters to the king to have the work stopped, and managed to succeed in their efforts for a short while.

From the start of the rebuilding to the completion of the temple, 49 years was the total. It is interesting that the Jews did not attempt to exaggerate their figures to Jesus, but referenced only the time taken in actual construction, not including the delays.

Conclusion

The temple's rebuilding occupied the full 49 years of Daniel's prophecy, with 46 years of actual construction and the remainder consisting of delays, particularly near the beginning of their work, when the rebuilding was put to a halt by royal decrees.