I am only an expert at removing the upper ones-----having done it myself. Use one of those cheap magnetic stud finder things---the kind that actually has a magnet in it---and goes erect when it passes over metal. Run it along the outside of the skin where the back of the bolt should be. Mark the four locations. Drill in those areas. You have a couple plies of fiberglass to go through, then foam. When done, you will have exposed the back of the bolt heads. When you put the bolts back in, you micro in a replacement foam plug then glass back over it (micro over the plug of course).
Joe Person (Varieze/Boeing guy) can give you detailed instructions for the match drilling that you will need to do. But I can give a quick summary below.
1st to remove the upper extrusions:
You will need to beat the upper extrusions out with a sledgehammer. You may need to dremel away some "boogers" on the longerons and surrounding area so that they will slip out rather easily. Even with getting all the epoxy/glass "boogers" off, it will take some rather hard hits with a sledge hammer. The motor mount side of the longerons will be pretty damaged after this process---however the end that attaches to the longeron and spar will be ok.
Match drill:
Make a jig out of smooth wood (MDF?). What you are going to do is glue and screw 2 pieces of wood together at 90 deg angles that you can lay the extrusions on. Need to build two jigs, one for the left and one for the left. Screw a stop block on the jig on the forward side that the extrusion will sit on (remember that the aft side of the extrusion will be bent and distorted after you remove). Clamp the extrusions in the jig and drill the 4 holes through each extrusion.
Now, way oversize drill the holes thru the jig. You need to get hold of steel bushings that you will place in the jig. The inner part of the bushing should be exactly the same size hole that was supposed to be originally drilled into the spar and longeron (check plans). Buy 8 cheap drill bits that are of this required size.
Put a big blob of bondo (don't use epoxy) in the oversized holes. Put the bushings into the holes (the oversized holes should be bigger than the outer size of the bushings so that you have some wiggle room). Clamp the extrusions into the jig. Put the drill bits thru the extrusion and thru the bushing. Wiggle the drill bits around to make sure that everything is nice and straight---everything should match exactly.
When the bondo dries, unclamp the extrusions. Now you have a perfect drill jig. Clamp in the new extrusions, put the jig in a vice, use the correct size drill bit (you now have 8 new ones) to drill the new holes. The bushings will give you the correct location and alignment of the holes.
Hope this helps