Japan locked itself down in 1663 and didn't open till 1853. So Japan would definitely not be doing any trading, at least in your trade. It would most likely be China, as long as their trips were far more frequent because they did visit America, but it took YEARS. I would suggest a route connecting to Russia before America if you want to make it a little more plausible. Also, I would highly suggest reading the book 1421: The Year China Discovered America to further solidify your query. I imagine it will provide loads of evidence and ways to alternate the history towards your favor.
On to your questions though! If you are saying thousands of years before, then the Native Americans would have become immune or died out. Also, this depends on the Chinese and what they would do. Would they enslave all the native peoples, making it far more likely for a widespread pandemic, or would they trade them as they did with the Europeans? And in most colonial situations the discoverer's people populate the land instead of the natives.
Well, the scenario I was thinking was that the contact would happen at the 1000's at the latest, so the 1663 lockdown is beyond the timeframe I'm aiming for. Now, I have read that there is evidence that certain indigenous peoples in Alaska and Siberia had loose and intermittent trade links, so the thought was that a power with the ability to construct slightly more durable ships would be able to make the trade more reliable.
Now, as for colonization I actually am leaning towards the Chinese for this given their lack of desire to be expansionist, or having the intermittent trade between siberia and Alaska become more stable and slowly involve other countries. In short the idea is that they will establish trading posts similar to the early European trade with Africa, so fortified settlements at major ports and defensible locations along the coast to trade with the natives, mainly for furs and the various resources of the coastal mountain ranges that are loaded with mineral wealth. I'm thinking a low steady amount of trade that sustains a few of these settlements along the Pacific coast, which can allow the natives to slowly learn east asian agricultural practices and other technologies, allowing for a massive population rebound once the initial wave of diseases push through them.
If I end up writing this into a story, I'm actually hoping to explore what a sort of synthesis of East Asian, probably Chinese or maybe Japanese, and the indigenous cultures of the pacific slope would look like, with influence spreading via osmosis deep into the continent.
Realistically the numbers coming over would be small enough that most diseases wouldn't have time to spread because they'd kill the ship's crews. If large enough numbers came over then there wouldn't be enough time for every group west of the Rockies (they'd end up colonised), but probably enough time for disease to establish itself in Mesoamerica and the Andes. Maybe Eastern North America too despite the lower population density.
Metalworking, or at least copper-working, definitely, since there was plenty of local use of copper (in the form of native copper) throughout the Pacific Northwest and Alaska. There was also iron salvaged from shipwrecks or traded across from Siberia but this was very rare. I think there'd be enough people striking it out on their own to blend into local groups as smiths, and they could probably help intensify local metalworking and maybe even introduce ironworking. These techniques could spread pretty far.
Livestock, possibly. The big one is horses which OTL spread fast in practically every place they were introduced. Most Chinese and Japanese horses were smaller than Spanish horses, but bring over some of the horses used by Turkic or Mongolic people and those should be very suitable. Other animals would spread slower.
Irrigation would be very questionable, but if there's enough contact with the Colorado River peoples who did use irrigation then it's certainly possible they'd borrow from Asian techniques. Other than them agriculture is very minimal to non-existant on the West Coast.
Writing I could see the same example as OTL where Cree syllabics and other similar alphabets spread very quickly.
OP said centuries before, so this would be Heian-era Japan which potentially did have the capability to explore that far, at least assuming they managed to subdue the Ainu and Kamchatkans first. I don't know if the institutions existed to permit such widespread colonisation. I think you'd have a few coastal settlements directly under Imperial control and plenty of settlements in the interior only nominally (or not at all) respecting the central government. Later I think China or Japan would establish true control.
Both the Chinese and Japanese (IIRC the vast majority of ships were Japanese) did historically "visit" the West Coast of North America before Europeans ever showed up but these were just fishing boats who were blown far off course and stranded there. None ever returned. Such a journey would not take years either, as the favourable sea currents in the Japan-Kamchatka-Alaska-West Coast arc is similar to the Gulf Stream in the Atlantic.
Yeah, I was actually banking on the favorable sea currents in the area reducing travel times enough that sustained contact would transmit the old world diseases without requiring the large numbers that turn the area into a settler colony. And thanks for the information on the native copper working, I knew that was a thing in the Andes but I was not aware of the practice in the northwest.
Right now I feel like the big issue is trying to figure out a way to establish trade links strong enough to transmit the diseases to the new world while being weak enough to not lead to an outright conquest of the pacific coast. So, with that in mind, maybe I will cut the Japanese out and have the trade be via the Kamchatkan people in Siberia to get the diseases and some basic things through to the natives before the Japanese arrive in force, giving them a century or three to rebound and adapt that will let them keep the Japanese confined to coastal enclaves when they do arrive. I know that's a lot to ask for, but I started this brainstorming with thinking about how the cultures of the Pacific Northwest would look with constant trade with Asia, so I'm trying to avoid situations where those same cultures are wiped out or subsumed by the Japanese/Chinese or whoever else spearheads the trade.
Anyway, thanks for the feedback! It's a really interesting topic.