Yz125 forks and triple clamp

Yes,

If you use the complete set, then yes, it should work. Most likely you can use the 99 triple clamps with the 2001 forks. Here's why.

The bottom triple clamp, and the lower fork tubes are the exact same parts with identical part numbers.
The upper triple clamp and upper (outer) fork tubes have a slightly different part number. It appears the only difference in the upper triple clamp is how the number plate is attached.
The fact that the lower triple clamp hasn't changed, means the outer fork tubes are the same diameter, and will fit.
My best guess is that you can just use the 2001 forks with the triple clamps and front number plate from 99.

Here are the comparisons:
Steering (Upper triple clamp and number plate):
1999
https://www.powersportsdiscount.com/oemparts/a/yam/500441e2f8700209bc78…
2001
https://www.powersportsdiscount.com/oemparts/a/yam/500446fcf8700209bc78…

Front Fork:
1999
https://www.powersportsdiscount.com/oemparts/a/yam/500441e2f8700209bc78…
2001
https://www.powersportsdiscount.com/oemparts/a/yam/500446fcf8700209bc78…