Stuck, routing speaker wire

What car? Sometimes you can push the wires through using a sharp point like a tip of a screwdriver. Just be careful. If not, do what you say and put some silicon caulk around to seal it.

Sure, you can drill new holes for it.  Use a length of small diameter rubber hose and slip it over the wire with the door open, and after the wire is inserted into the door push both ends of the rubber hose firmly into the two holes.  Or you can use grommets for the holes...or the dirty way is to wrap the wires in electrical tape and use silicone caulk in the drilled holes.  Just as long as the wires are protected from abrasion.

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Build the box so that it performs well in the worst case scenario and, in return, it will reward you at all times.

If you absolutly can not fit it through the factory boot, you can always purchase a boot that is similar to factory on to run your speaker wire through or just as you described cutting into the seals.  It is wise to silicon the area around the speacker wire and the seal and make sure you run from high at the car body to low at the door so any water might run into the door not the kickpanel where many important vehicle electronics are placed.  Good Luck!

Thanks...     Stevdart, I am assuming that rubber hose is a good idea just to help with the seal overall.  I am using twisted speaker wire so the outside layer should provide some protection for speaker wires.   

get yourself  fiberglass fish cable and a little gel and you should not have any trouble getting wires through boot take your time. the boot made be  ribbed and that's where your getting snag

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2-alpine amp mrv-f545 4ch amp
polk audio 6 1/2 frontdoor w/alpine center speaker
polk audio 6 1/2 rear w/8"polk sub
2-12" alpine X type sub
2-alpine mdr-1005 amps

Thanks all.  I cut new openings in the rubber boots and actually used a 26" road bike inner tube to insert wires and seal holes.  Since I was bi-wiring, I don't know how else I would have done it.