I hope these few hints help you with your build. Others who read this thread may be able to provide other tips to help guide you along too. I learned these tips after discovering the issues the first time I built the kit. I've even got a third in the stash.
First off, one of the things you'll want to do is sand off the little nub (an IR sensor) on the front fuselage near the spot where the windscreen will fit. It wasn't present on Canadian Starfighters and I'm pretty sure they weren't on USAF jets either. I believe it was only on Starfighters used by European allies Germany and Italy. I stand to be corrected though.
You can see that the front fuselage assembly is top and bottom while the rear part (vertical stabilizer / exhaust opening) is left and right. An odd design but the front halves fit together well, as do the rear halves. The big problem is that when you glue the back part to the front part, there will be a step joint between the pieces. To help eliminate this step, glue the front parts together as normal. On the rear parts, glue the top seam and the vertical stabilizer together and don't put any glue on the bottom seam. This will allow you to glue the back to the front a bit at a time. I use Tamiya Extra Thin Cement. It's strong and dries relatively quickly.
Before you glue the front and rear halves of the fuselage together, the long seam on either side of the front fuselage will need some putty and sanding otherwise it will be really prominent.
Align the front and rear fuselage parts along the spine and only glue one side of the rear assembly to the front and let it dry thoroughly. Once the glue is completely dry, glue the other side of the rear to the other side of the front assembly. Leaving the bottom seam of the rear assembly unglued will allow you the gently spread the pieces to ensure that the fuselage joints line up on the front and rear sections thus eliminating the step. Once the front and rear sections are glued together, you can glue the bottom seam of the rear section together. There will be a small gap along the bottom of the rear section near the spot where the front and rear sections join that you can fill with a bit of putty and then sand it smooth.
A friend who flew CF-104s told me that the speed brake doors were never open when the airplane was parked on the ground unless it was undergoing maintenance. You can pose your jet with the brakes open if you wish but if you're going to pose them closed, the fit of the speed brake door into the opening on the fuselage is a bit tricky. You will need to cut off the three 'fingers' on the speed brake door and you may have to sand off or eliminate some of the detail in the speed brake well or on the inside of the speed brake door in order to get them to be glued into place properly.
On the bottom of the forward fuselage, behind the front landing gear bay, there are a bunch of vents and behind the vents is a slot for a shell ejection chute (part 38). Don't install that on your build. Again, CF-104s didn't have them and I don't believe USAF jets did either.
There are two seats supplied with the kit, parts 34 and 51. Part 34 is the seat you want to use if you're building a USAF or Canadian CF-104.
If you plan on closing up the cannon bay with the cover (part 14), glue the cover in place before gluing the top and bottom fuselage halves together. Also, leave out the cannon bay (part 47). It will make it much easier to glue the cover in place. Having said that, you'll need some putty to fill the seams of the cover in place because part 14 don't line up exactly on the fuselage.
Apologies if this seems long-winded but these are the really major issues / problems I discovered while building this kit and the solutions I used in fixing them.
Best of luck with your build and I look forward to your progress.