Glad you found the problem! It's very common in new builds so I threw it out there just in case.
The 5k6 resistors are very good to have. They are called "grid stoppers". They will have no negative effects on the tone/feel of the amp. In fact you can go much larger in value before noticing any high frequency loss. Basically, they interact with the internal "miller capacitance" of the tube to form a low-pass filter which rolls off very high frequencies above the audible range (radio, etc.). This can help prevent oscillation and red-plating tubes among other things. It's best to put them right on the tube socket like you had.
Regarding break-in time, the amp (mainly signal capacitors and OT) will gradually settle in within about 20 hours of use. You may notice it becoming "clearer", "tighter", more "musical" for lack of better terms. Speakers can take longer, depending on what you have and how loud you play.
I normally wouldn't post a quote from another site but Aiken's site (
http://www.aikenamps.com/" onclick="window.open(this.href);return false; ) currently has it's links messed up. Below is a quote from him about grid stoppers, which is very informative.
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From aikenamps.com:
Grid Resistors - Why Are They Used?
General
If you look at the schematic of a typical guitar amplifier, you will notice that there is a resistor in series with the grid of the first tube, usually around 68K or so, and there is also a resistor in series with the grid of the power tubes, usually 1.5K or 5.6K, and you may occasionally see very large value resistors, such as 470K or greater, in series with tube grids in high-gain preamps. Some amplifiers have no such grid resistors, and occasionally people will recommend removing them to supposedly "increase the gain" of that stage. What is the purpose of these resistors, and should you remove them?
Reasons for the resistors
These resistors, which are commonly called "grid stoppers", are not put on the control grid of the tube for signal level attenuation purposes; rather, they act as a very high frequency low-pass filter in conjunction with the input capacitance of the triode (which is the sum of the grid-to-cathode capacitance and the Miller capacitance, and can get as high as 100pF or more). In the normal operating mode of a vacuum tube, the grid is biased negatively with respect to the cathode. Because of this, there is no current flow into the grid element, and it looks like a very high impedance circuit node. This means that there can be little or no midband attenuation of the input signal, because the voltage divider formed by the series resistor and the high input impedance of the tube is very small. For all practical purposes, the attenuation is negligible at midband, so there is no "increase in gain" by removing these resistors. Attenuation only occurs at the higher frequencies, above the frequency breakpoint caused by the series resistance and the input capacitance.
The grid resistor accomplishes the following things:
It helps prevent high frequency parasitic oscillation in the tube itself
It helps prevent radio frequencies from getting into the input stage, where they can be rectified and lowpass filtered (AM detection) and become audible at the amplifier output
It can limit grid current when the tube is driven into the positive grid region, which helps in preventing "blocking" distortion
Where to put the resistors
In order to take advantage of the parasitic suppression benefits of these grid resistors, they must be placed as close as possible to the socket pin of the tube, preferably soldered directly to the pin with a very short lead. The resistor should be placed after the grid-to-ground resistor (usually 1 Meg or so), to avoid attenuation and to keep the signal path short. If the resistor is connected in series with the input jack and before the 1 Meg grid resistor, there is a small loss of the input signal, although, in most cases the attenuation is not enough to be concerned with (0.94 times for a 68K grid stopper and a 1 Meg grid resistor), and in amplifiers with a high and low level input, the grid stoppers also serve as attenuators. When designing an amplifier, it is better to use separate resistors for input attenuation purposes in order to be able to locate the grid stoppers as close to the input grid pins as possible, rather than mounting them on the input jacks.
How large should they be?
The grid resistor value typically varies from as low as 1.5K to as high as 470K.
Most output stages use relatively small grid resistors, such as the 1.5K seen on the grids of 6L6 tubes in most Fenders, and the 5.6K seen on the grids of EL34 tubes in most Marshalls. In general, the grid resistor at the grid of the power tubes can be as high as 56K to 100K before any noticeable loss of high frequencies occurs. Higher values can help in reducing "blocking" distortion as noted above, and can also take some of the "edge" off of an overly brittle sounding output stage. If the resistor value is made too low, it may not be enough to prevent parasitic oscillations, and the amplifier may exhibit instability in the higher frequency range. This may or may not be audible. Symptoms of oscillations include: high-pitched "squeal", glowing plates at "safe" bias currents, harsh treble response, lack of power, undesirable overtones, and unusual frequency response which makes the amp sound funny. Note that power tubes have a specification for maximum resistance that can be in series with the grid terminal before the tube becomes unstable due to grid current. The maximum allowable resistance is larger in cathode biased circuits than it is in fixed bias circuits because the cathode bias provides some "self-limiting" protection against bias runaway. The total resistance is the sum of the series grid resistor and the bias feed or "grid-to-ground" resistances, so if the max spec is 300K, for example, and there is a 220K bias feed resistor, the largest grid resistance that can safely be used is 80K. Of course, in practice, tubes should not be run that close to the edge of their specifications, to insure reliability.
The grid resistor on the preamp stages typically ranges from 0 to 68K, although very large values, such as 470K, are sometimes used in high-gain preamps to shape the frequency response and prevent "blocking" distortion in the preamp section under heavy overdrive conditions. The Miller capacitance of a typical 12AX7 is around 151pF, so the upper frequency response -3dB cutoff point of a stage using a 68K grid resistor is around 15.5kHz. The frequency response drops to around 2.2kHz if a 470k grid resistor is used. This "free" response rolloff can be used to tame the "buzziness" of high-gain preamp stages without having to add additional rolloff capacitors. Perhaps the most important grid resistor is the one that goes to the grid of the very first stage, right after the input jack. This resistor is the one that prevents oscillations and pickup of radio stations and other noise due to long or poorly-shielded cables. It is not usually a good idea to eliminate this resistor. Ideally, it should be soldered directly to the grid pins of the socket, with very short leads.
