I had the same problem on both my 16LT and 17LT, with three of the four bulkheads not fitting very well.  If your other hull measurements (especially width) are correct and the hull otherwise has a good shape, you do not want to pull the side panels in tight against the bulkheads.  This will distort the hull and cause a dimple in the sides. 

The bulkheads do not really need to fit that well as long as they are close enough that you can filet them to the hull.  For the forward bulkhead, you can move it forward or back a little to find the best fit.  The position of the aft bulkhead is pretty much set by the cockpit location.  Trim the bulkheads if that helps the fit or even add a little wood along the side if needed.  Once you get the best fit that you can, filet the bulkheads in place.  If the gaps are really wide, use a  little tape on the back side to prevent the peanut butter from oozing through until things set up a little.  Thick filets will be plenty strong but do add weight.

I am not an expert but this worked for me.

That blasted "spreader stick," which the instructions have you placing in the Chesapeake-series kayaks with considerable ceremony, seems to be the cause of much bulkhead-fitting frustration.  

I've built more than a hundred of the Chesapeakes myself in classes, and found that if I remove the spreader sticks as soon as I insert the bulkheads, then the fits were greatly improved.  

The spreader stick's only real utility is in holding the side panels in approximately the right shape while the bottom panels are stitched on.  And there its utility ends.

The upshot in removing the spreader stick early is a slight variation in the finished beam (width) of the hull, but this is all above the waterline and makes no difference in either appearance or function.  

See the video around the 4:25 mark.

I am nearing the end of construction of my 3rd CLC boat which is a Ch16.  The first boat was a Ch17lt and the 2nd was a WD 12 Hybrid; both from plans.  For the latest Ch16 I decided to go with the full kit rather than making the parts myself. 

With the 17lt, the first set of bulkheads I made from the plan sheets were close but I ended up re-fabricating them a second time slightly larger so they would fit perfectly in their designated locations.

With the latest Ch16 kit, I managed to get the supplied aft bulkhead to fit nicely but not the forward bulkhead.  I ended up moving the forward bulkhead toward the bow about an inch to reduce the space between it and the hull panels.  All of this of course with the spreader stick in place.  This all worked out well until I went to install the forward deck that came with the kit.  No matter what positions I tried, the forward deck was just slightly too narrow at the deck beam and cockpit to cover from side panel to side panel.  To make things work, I shaved the top of the deck beam about 1/4 inch to allow the deck to reach the sides.

As I look back on it, I think moving the forward bulkhead forward caused the beam in the forward area of the cockpit to be slightly wider than designed even though I still had the spreader stick snug in place toward the rear of the cockpit.  A small variation in the height that the deck beam gets installed relative to the shear clamps compounded the problem.  It would be nice if the forward deck part was just an inch wider at the cockpit to allow for these variations in construction. 

If building from a kit again, I will temporarily fit the deck beam and use a string to measure the side to side distance over the deck beam before committing the bulkheads or deck beam to epoxy.  That way I can be sure the forward deck will be wide enough when its time to install it.  If there's an issue, it can easily be fixed before things are epoxied.

All in all, these challenges and their solutions just add to the intrigue and enjoyment of building your own kayak.