I am not an expert but have built both the 17LT and 16LT. With both of those kits, fit of the bulkheads was much as you describe.  After learning some lessons the hard way on the first boat, I got the second one right.  Here are my suggestions.

1.  Placement (fwd/aft) of the aft bulkhead is pretty critical beacuse it needs to be matched with the cockpit opening.  The forward bulkhead is less critical as long as it won't interfere with the foot braces and your planned hatch location.

2.  With the bulkhead placed fwd/aft, you want to raise them up so that they are against the bottom of the shear clamps.  It may take some trimming.  Not a big deal if you have larger gaps along the hull sides/bottom because they are easy to fix with a large filet. 

3.  You also want to make sure that he top of bulkheads are high enough that they will support the deck when installed.  Use the planing guides to make sure that they are high enough.  The bulkheads should be a bit above the planing guide because you will be removing the outer edge of the shear clamps when you plane them. 

4.  After you plane the shear clamps, use the planing guide to trim/sand/plane the top of the bulkheads to the correct height/shape.

5.  If you end up with a bulkhead that is not high enough, you may have to add some height.  On my wife's 16LT, the aft bulkhead was 3"+ too short.  I cut an unsued hip brace in half and glued it to the bulkhead for additional height.  The picture below shows the bulkhead before I added the extra height.

6.  If you are concerned with strength, you can add a strip of fiberglass over the larger gaps. 

7.  In the end, it really does not matter how pretty they are because you can't really see them except for the forward side of the aft bulkhead.

Hope that this helps.

i have built several 17LTs a while ago.  my recollecton is that fillets were needed and the fit was less than perfect.  that said, i don't recall that they were that far off (i.e., 3/4 inch)

as Sun indicated above, the bulkheads can be moved around a bit but the key thing in moving them around (if that is the route you choose), is to make sure you don't impinge on the cockpit space.  in addition, you do want, in general, to have the rear bulkhead proximate to the rear of the combing to ensure strength in that area.  in entering/exiting a kayak, you can put a lot of compressive force on the rear combing and if the bulkhead is not there, you would need some other reinforcement.  so as Sun said, there is more flexibility to move the front bulkhead around.

fwiw, it would not take more than a couple minutes to call CLC and confirm you have the right bulkhead.  they can give you a quick measurement (e.g., max width, max height) you can use to test the parts you have.

i do remember in my builds that all hulls did not bend when wired up exactly to the expected widths at key measurement points.  CLC can give you the station measurements and confirm the widths so you can then decide if you want to let the hull be relaxed a bit more (and use fillets) or to tighten up the boat to be right on spec.   they can also probably give you a bit of guidance about how far off is so far off you want to pause and correct it.

best of luck...the 17LTs are great boats.

Howard