Tl; dr: I'm afraid you can get the official support from the Jesuits to get to Japan at least in a few years (until ca. 1633) on condition of your education and expertise.
First of all, why Matsumoto (now the biggest city in Prefectural Capital of Nagano, Central Japan)?
While Matsumoto certainly has a famous extant castle from ca. 1600 now, it attracted almost to none attraction from foreign sources at that time. From a historical point of view, Nagano Pref. did seldom constitute a single political-administrative unit prior to Meiji Restoration in 1868, especially during Edo Period. Several clans/ daimyos divides mountain regions of Now Nagano Pref., and one of them were Sanada family who ruled Numata (Gunma Pref.)-Ueda at first then was transferred to Matsushiro in 1620s. Clan Matsumoto and its (Clan) Capital, Fukashi-Matsumoto was at most one of the local power centers, probably not the biggest city with a political and economic function in now Nagano Pref then.
Clan (district) Matsumoto itself saw changes of ruling family: Warlord (daimyo) family Ishikawa who built the famous Matsumoto Castle (in extant form) in fact had difficult relationship with Tokugawa Ieyasu. Warlord Kazumasa Ishikawa (d. 1593) had originally been a trusted subordinate of Ieyasu, but later he deserted Ieyasu with a not so certain reason and instead run out to Hideyoshi Toyotomi (Hashiba) in 1585 (, and was later granted Matsumoto by him). His son, Yasunaga, was reconciled with Ieyasu, but again Ieyasu confiscated Matsumoto from Yasunaga in 1613 due to the possible involvement with the plot (familial relationship with the alleged schemer, Nagayasu Okubo). Ogasawara, then Toda (Matsudaira) family came to rule Matsumoto successively in 1620s and 1630s. While neither of Ogasawara and Toda family seemed not to rule the clan on tighter grip yet, Matsumoto would certainly not be a focused target for the mission in central Japan.
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On the other hand, as you know, Tokugawa shogunate had implemented the the prohibition on Christianity since 1612-14, and the Society of Jesus (Jesuit order) also had to retreat [most of] their official ecclesiastical functional organization out of Japan then moved to Macau. About the same time (ca. 1612/13), the Christian missionary activity in Japan was plagued by different levels of factional disagreements and power struggles, such as 1) among the different actors of missionaries, such as the Society of Jesus, the Franciscans, the Dominicans, and the Augustinians, 2) the discord between the Portuguese and Spanish Jesuits, and further, 3) European padre and possibly also Japanese Irmão (lesser clergy). These disagreements, together with the succession strife of Nagasaki province, the center of the church organization in Japan, hindered the Catholic missionaries to take an unified and swift counter-measure against the shogunate's Christian policy.
Anyway, the Society still retained, or selected a small number (27 against 115 prior to the expulsion) of Jesuits to keep on their activity 'in secret'. Interestingly enough, the Portuguese members of the Jesuits were prioritized to this selection (Takahashi 2019: 367f.).
Of 18 padre ('Father' - superior rank of the clergy) in 27 members:
Another source for 21 underground padre from 1615-1621 also confirms this trend:
Takahashi supposes this bias probably came from the fact that the Portuguese superior (Valentin Carvalho, d. 1630) involved with the selection, with the following apparent criteria:
Then, the first and foremost problem for OP would probably be how to meet these criteria as well as the Portuguese favoring personal assessment by Carvalho the Portuguese as a young and inexperienced Italian Jesuit.
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The following brief answers to Op's individual questions are very roughly based on the career of Father Bento Fernandes (d. 1633), the Portuguese Jesuit who was active in the underground Christian mission around 1620 as well as a colleague of famous apostate Father Christovao Ferreira (Barros Rodrigues 2007).
How do I get there? Will I travel alone?
After the large-scale expulsion of European missionaries, Macau and Jesuits maintained a trade with Nagasaki in 1620s and early 1630s, mainly handling raw-silk (Oka 2010, Chaps. 4-5). This trade invested both from Japanese (warlords, merchants) and Macau side (merchants), and its profit was used to maintain the administration of the missionary activity on field as well as of St. Paul college of the Society [of Jesus] in Macau. While officially the entry of European missionary was prohibited, you might be able to get on board of this ship at least halfway to Japan (then to take a little boat).
Before the prohibition, OP might have had a better opportunity to have a Japanese companion, as the early career of Father Fernandes suggests (Barros Rodrigues 2007: 98), but he also mainly seemed to act alone in disguise in Japan after the prohibition.
What was my training in Europe?
The missionary didn't have to get trained for all the requirements in Europe.
To give an example, Fernandes had rather had an ordinary education in humanities in Portugal before he joined in the Society.
The Jesuits had a few colleges at their base in Asia, and OP even had a opportunity of learning Japanese from someone who had been expelled from Japan in Macau. They also published a few Portuguese-Japanese dictionary as a kind of textbook. Then, the problem arises: To what extent is it more difficult for an Italian to learn Japanese than for a Portuguese, with this Portuguese-Japanese 'dictionary'?
It generally took a few additional years to study theology and others, including the local language, in such a Jesuit college in Asia before going to the actual field of mission. Fernandes got ordained as a priest not in Europe, but first in Asia (probably in Goa, India) (Barros Rodrigues 2007: 97).
How do I get food during my travel?/ How can I communicate with the people of Matsumoto?
OP should not have expected to exchange foreign money with food without danger of being reported, and bad-Japanese would also led to being reported. In short, Japanese only (both in money and in a daily language). This is probably partly why Carvalho included Japanese proficiency as one of the requirements to spy in Japan.
How many people will I likely have converted in the first year in Japan?
Jesuit annual report for the year 1621 states that Japanese Irmão called Martin secretly visited a few Christian havens across Eastern and Northern part of Japan, and converted 66 in total in Edo and in Numata, Gunma, and 27 in northern Japan (probably in now Nigata Pref.) (Hirayama 2016 - citing Girolamo Maiorica, Italian Jesuit's letter to Superior General, dated to Oct. 06, 1622, from Macau).
I think it was extremely unlikely for a newly visited foreign missionary made a great success than this case.
As for Fernandes' case, He also took a visit in Numata, Japan in 1620, and was said that many people heard of his preach that led to three young samurais' baptism in the household of Warlord Sanada, that is to say, Nobuyoshi Sanada, son of Warlord Nobuyuki Sanada (d. 1658) of Clan Numata-Ueda, elder brother of famous samurai, Yukimura (Nobushige) Sanada who opposed vehemently against Shogun Ieyasu Tokugawa in the siege of Osaka in 1615 (Hirayama 2016, citing Jesuit annual report for 1620).
Hirayama also a bit hesitantly supposes that Nobuyuki and Clan Numata (Gunma Pref.)-Ueda (Nagano Pref.) unofficially/ de facto tolerated a spread of the Christianity at least until the 1620s due to Jesuit's association with the advanced European mining and civil engineering technology. After the transfer to Sanada family to Clan Matsushiro in 1622, some Christian subordinate samurais also followed Nobuyuki to Matsushiro, now central Nagano Pref., and settled then. Even Clan Matsushiro had to adapt more strict ban on Christianity in accordance with the shogunate's official ban in the beginning of the 1630s.
When Father Fernandes (and Irmão Martin) took a visit in Numata in 1620, however, there had already been a Christian congregation there. They rapidly got popular under the guidance of a mysterious Japanese missionary, called Toan (been active since ca. 1614-30?) if we believe later Japanese source, but his exact provenance as well as his official collaboration with the Jesuits remains unclear.
Since 19th century, both European and Japanese classics have noted a few Christian centers in now Nagano Pref., mainly Ueda(-Numata), Matsushiro and Takato in SW Nagano Pref., and two of them (Ueda and Matsushiro) were associated with these late Christian demography under the rule of Warlord Sanada in the early 17th century, not earlier.
How dangerous is my whole endauvour?
Very dangerous (more than dozen of ca. 50 Jesuit missionaries were captured and many were martyred before 1639, the beginning of the so-called 'Sakoku'). I don't think OP will survive longer than either Father Fernandes or Ferreira, captured in 1633.
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