no sound on input 3 and 4 and midi problems!!!!!!!

[seasondigital]

First of all, here is my history. I purchased pro tools 5.3.1 for windows about 3 years ago and it worked fine up until about 6 months ago. The problems that started occuring were the cpu would sometimes just shut down in the middle of a session. This happened a few times until one day it just shut down and would not power back on. I took it to a computer guy and he said that my motherboard was fried. Since my version of pro tools was old, I upgraded to pro tools 6.4 and purchased a chipset and processor that would work with it. I have my system up and running with the newer version of pro tools, but I have two problems that I can not fix. When I was running pro tools 5.3.1, I had pro tools as the master midi controller with my trition extreme being the slave, running thru to my akai mpc 2000xl, and it worked fine. Now when I set it up exactly the same way, my triton is not getting the signal from pro tools. Secondly on digi 001, the 3 and 4 inputs are not registering any sound when audio is played thru them. Inputs 5/6 and 7/8 and also the 2 mic inputs are working fine. Is there a chance that my pci card or digi 001 was damaged when my mother board got fried previously or are there simple settings that I am overlooking? Is there a test that I can run on the system to determine any damage? Since I am using the triton, the mpc, and a sound module, all 3 of my audio imputs are extremely important. I would appreciate any help or assistance.