dont't make clean and make mrproper. This would force you to do a completely new configuration.
Another thing is that afaik ext3-support depends on ext2-support. I think that it is not possible, that a kernel supports ext3 without supporting ext2. The ext3 is a ext2 with an added journaling.
Maybe that your errormessage at boottime points you to another problem.
Here a part of the kernelconfiguration-helpmessages regarding to ext3
...Other than adding the journal to the file system, the on-disk format
of ext3 is identical to ext2. It is possible to freely switch
between using the ext3 driver and the ext2 driver, as long as the
file system has been cleanly unmounted, or e2fsck is run on the file
To add a journal on an existing ext2 file system or change the
behavior of ext3 file systems, you can use the tune2fs utility ("man
tune2fs"). To modify attributes of files and directories on ext3
file systems, use chattr ("man chattr"). You need to be using
e2fsprogs version 1.20 or later in order to create ext3 journals
(available at <http://sourceforge.net/projects/e2fsprogs/>)...
So it may be a good idea to change your /boot-partition to ext3 instead of building a new kernel.