Is the stock 2.6.9-42.EL kernel compiled with ISA support? Do i need to rebuild the kernel by hand? Is there anything I need to do to enable ISA support in CentOS4.4? If I do need to rebuild the kernel, what
Nope. The kernel was built without isa support. There was a mailing list thread a while back (the exactly link escapes me) which explained how to rebuild with ISA support specifically, however the wiki (wiki.centos.org) contains the steps needed to build a custom kernel.
Support for ISA may have been built into the centosplus kernel by Johnny, but I honestly can't remember if he did that or not.