I have about 45 machines connected to my RouterOs each us DHCP to get ip addresses, i assigned each machine a different bandwidth limit, i assigned one machine a static ip address and i changed the arp entry for that ip address to the mac address of the same machine, so generally i assumed that this machine would not be affected by the queue limits in any way . but i found out that the traffic to this machine is affected when the network load is high and even accessing the router through that machine using winbox or the web interface during that time is a struggle ... so is there a way to make this machine prioritized during the peak time or something ?

Start by upgrading to a legal ROS license.

my licence is not legal ?

It may come as suprise, but it's quite likely.
Let me guess. Is it x86? Is it L6? Does it have extra-channels? Is it impossible to upgrade? If you answered YES to all questions, then your final answer is also YES.

v2.9 is not supported anymore - it's too old. please upgrade: http://wiki.mikrotik.com/wiki/Upgrading_RouterOS

if i backed up my configuration and i installed the ROS 4.5 version, will i be able to import my configs to it ?

If you upgraded normally as per instructions, your config should stay as it was