Animating the transparency will be a piece of cake.
in hypershade, create shader for your intestine, apply shader
create ramp and drop it on shader and select the tranparency channel
select shader and under hardware texturing select transparency channel and crank up the quality
enable hardware shading in your camera view
this should now show the red, green, blue texture on your object.
if the ramps 'rainbow' is going the wrong way 'width-wise, vs lengthwise' change v-ramp to u-ramp
now, you will need 2 colors on your ramp, so delete one of them and change the other two, one to black and one to white. Adjust their positions so that you see in the shaded viewport that most of the intestine is white, with just a little tip of black. Now at frame say 0, set a key for both of the color positions. go to frame say 100 and then adjust the color positions so that nearly all of the intestine is black, with just a little tip of white at it's other end. Now key both of the color positions.
and there you have it
now, here's the rub. Just because an object is transparent does not mean you can't see it (think glass). So, what you need to do is kill the highlight on your shader (if it is not a lambert) this is easiliy done by taking the output of your now animated ramp into a reverse node, then plugging the output of the reverse node into the specular color of your shader.
hope all of that helps
have a lovely day