Doing the match, a 6" to a 9" drop with a 40 inch driveshaft, you'll see the splines pull out .56". With mine lifted 3" in the rear I still have 1.75" of safe extension and 1.75" of safe compression room so lifting put my driveshaft dead center in it's safe travel zone.
And BTW, the OP hasn't had any problems with his short driveshaft, which is about 2" shorter than mine, other than the normal grease-related problem.
Plus if you buy a longer driveshaft for lift compensation you will risk over compressing when you bottom out the suspension.
Where did the the op post measurements that are shorter than yours? I must have missed that.
If you mean front driveshaft by shorter driveshaft then the front goes to a fixed pumpkin that doesn't change with a lift, hence no need to change driveshafts.
What you really need to be concerned about being centered in the slip yokes with is suspension travel. Do you have the same amount of up and down travel? Then the slip should be centered. Not many vehicles have that articulation centered constantly. If you can droop 5 inches but only uptravel 2 then no, your slip yoke engagement is not correct. There is a lot of geometry involved with suspension, starting with accurate information on a case by case basis is crucial. That's why wheel spacers tax your steering components more, throws off the scrub radius geometry but what I mostly hear people talk about is added stain to the hubs.
When you order a driveshaft you measure everything out, you don't just guess at how long and see if it bottoms out or falls out.
Pull the springs and put it through a full articulation measuring distance as you go. Pretty hard to not get the right one if you know what your doing. That's how custom trucks get built by some people, everyone has different styles right?
Your truck at 3" lift is going to be different than the op at 4.5 inches of lift. Can you guarantee your rear end is at the same spot his is ? Links can be stretched, bent, distorted or some other issue that locate his rear end slightly different than yours. Maybe yours is a hair forward and his is a hair back. You just don't know that looking at your computer, things need to be accounted for in the real world.
Not trying to be a jerk or start a fight.
I hope the op goes to a driveshaft shop and just gets it checked out, it can't hurt anything and might possibly surprise everyone on the forum if they come back and say yeah, you need to stretch this. And I might be surprised when they say no, it's fine. And I'm done here now, good luck with getting it corrected!