i tried talking to the hosting provider bout this and they blame SMF instead, saying it's a common issue with SMF. they refuse to increase the wait_timeout value.
While it is a common issue with SMF, you'll find that it's a huge issue with really poor quality hosts. It is especially a huge issue with GoDaddy. Actually, there are few hosts outside them in particular that I've seen as having this problem. Heck, even with 1&1 (an awful host in my opinon - I manage an SMF forum that is hosted with them), I haven't seen this issue.
Note that since SMF does some other things including DNS reverse lookups while the MySQL connection is open, a really bad DNS server can cause this issue. You can try disabling lookups and see if that helps.
so, i'm kinda wondering if it's possible if i made a copy of the database and import it to another server. and instead of connecting to the database from the localhost, can i link my forum to the database on that other server instead.
Only if the owner of that server allows MySQL connections from your web server. Most of the time, MySQL connections are blocked from anywhere except the host the server is with.
This might not be a good solution, however, as the extra time it takes to contact the outside server might cause large slowdowns of page generation or even further problems.