A lot of the 4-to-1's I've seen are as you describe. Both myself and my uncle have K3's and I've seen both configurations, my bike with stock and his with aftermarket. The little spigots on the cylinder head are are each held in place with 2 countersunk phillips-head screws. The aftermarket exhausts do away with the whole works, bolting directly to the head as opposed to clamping onto the spigots, like stock pipes. Seems a bit redundant to me, and it must have to Honda as the design was later changed to having studs in the head with nuts that retained the half-moon clamps and clamp as frostypuck described.
OK, so now that we covered the history lesson, what do we need to do? Are there any parts of the crossed-slot left in the screws? If so, you can get an impact driver from Sears and remove them. You just place it on the screws like a normal screwdriver and smack it with a hammer. If there is nothing left of the slots in the screw head, you'll probably have to drill the heads off the screws, enabling you to remove the spigots and put vice-grip pliers onto the leftover screw sticking out of the head. Sears also sells a kit for removing damaged phillips-headed screws which has left-handed drill bits, so when the bit digs into the screw, it can back it out. Use a pick or screwdriver to dig out the old copper exhaust sealing rings from the cylinder head. You'll want new ones (You might already have them, but you didn't mention them) and they are available from cycle recycle, partsnmore, and all kinds of other internet suppliers. Now, most of the aftermarket 4-to-1's I've seen have flanges that don't butt directly up to the cylinder head, so you will probably need longer screws. If you have new phillips-head screws, take one with you to a hardware store and buy a set of allen-headed metric bolts with the same size and type of threads. This way you won't have to deal with stripped-out screws again!
Others might post some ideas for removing the stripped screws, so you might want to look at more options before tearing into the job, as if the screws break off flush with the cylinder head, it will be lots of fun trying to remove them then! (Read: major work involved!)
Good luck with it and let us know what happens.