first of all you don't want to be radiating a kilowatt signal into a room you are in (or near for that matter)... you can cause tissue damage to yourself, and one of the first place this shows up is in your eyes in the form of cataracts. also be aware that your waveguide extension was unterminated, and depending on the actual length of it could cause a serious impedance mismatch, which is not good for the magnetron. every dimension inside a microwave oven cavity is a carefully calculated thing. if you look at metal racks for use inside the oven, they all have identical dimensions for the length and width of the gridwork, which is actually a series of 1/4 wave shorted stubs (which is a high impedance at 2450Mhz), which will absorb very little energy. there is an analogy with the waveguide as a series of quarter wave shorted stubs, where you begin with an open wire transmission line (2 parallel wires, in this case they are also 1/4 wavelength apart). then supports are provided to hold the two wires 1/4 wavelength off the ground, and the supports are made of 1/4 wave shorted stubs, which allow the wires to be supported, and the shorted ends of the stubs can be laid on a grounded surface without affecting the signal on the transmission line. for added strength, the vertical sides can become metal walls, and the short circuit of the stub can become a metal floor, so you end up with a solid U shaped channel. for protection against weather, an upside down channel of the same dimensions can be laid on top of the channel, so now you have a piece of rectangular tubing with a 2:1 ratio of height versus width, and this is a wave guide.
one thing required to efficiently couple a wave guide into open space is some way of matching the impedance of the waveguide to that of open space, the simplest way to do this is the use of a horn antenna (the "funnel" you mentioned) if you don't have this at the end of the waveguide, some of the signal will be reflected back down the waveguide to the magnetron, and can damage the magnetron.
to protect yourself, the best thing would to run your experiments inside a faraday cage made of metal window screen (with the screen grounded)... with you outside the faraday cage...