I am building an LT-40. Finished the left wing perfectly, then started on the right. I chopped the main spar and rear spar off at the ends as the instructions called for. Then I went to line up the pre-grooved trailing edge and it didn't line up with the plan this time. To make a long story short, I had to razor saw about a 1/4 inch off the scrap wood that I had previously cut off of the main and rear spars and CA it back to the ends to make the spars long enough to accept that that W5 rib.

Has anyone else has this problem?
Will the CA'ed ends be as strong and secure as if the wood were long enough in the first place?

Generally speaking the joint will not be as strong as the original piece of wood. I am not familiar with the LT 40 but if you can put the joint at the outboard end of the spar it probably won't be significant. Also you can put doublers on each side of the spar joint. A piece of 1/8th balsa about 1/2 inch long ought to work. End joints on spars are usually done with a "scarf" joint. It is a diagonal cut with the length about 5 times the height.