Chefg1 -- If you are using 8 ohm speakers with the unit set up for stereo, they should be connected to the "25 volt" output tap. In this mode of operation, these taps represent a 6.25 ohm winding, which is the closest you will get to a true 8 ohm tap on this amplifier in stereo mode.
While each channel is in deed rated to deliver 100 watts RMS with stereo operation, this would only be true if a load of 6.25 ohms were applied to the 25 volt taps. When an 8 ohm load is used, it produces a power loss -- in this case, reducing power output to 78.1 watts RMS per channel. In actual practice, the slight loss is hardly noticeable, and many speakers -- nominally rated for 8 ohms -- have impedance dips below their nominal value anyway. Making sure you have the amplifier/speaker combination properly connected is the first step in tracing your distortion down.
As for the use of 6550s, they are indeed a very good tube substitution for this amplifier -- from the standpoint of output tube loading. In this regard, I am not sure what information drtechno is basing his information on with his recommendation of 6L6 class tubes, but they would be a very poor choice for this amplifier at the screen voltages this amplifier operates at. At 335 vdc, these tubes simply could not pull the peak currents required for the loading conditions presented, so that power output and distortion would both suffer significantly. On the other hand, 6550s are easily capable of the required currents, and more.
However, regarding drive voltage, Battradio's concern for having adequate drive available for 6550 tubes is well founded. The conversion from 8417 tubes to 6550 tubes will require about double the bias voltage, and therefore about double the drive voltage. While the original driver circuit is very capable for 8417 tubes, it is very marginal for 6550 tubes if full power is routinely required at low distortion -- especially on the low end of the frequency spectrum. The changes necessary to insure adequate drive for 6550 tubes principally involve raising the B+ to the phase inverter stage to increase its peak output capability. This should be rather easy to do within the framework of the original design.
Finally, since the Gm of a 6550 is about half that of an 8417, a change to 6550s would also require an adjustment to the NFB circuit to restore the original feedback level when 6550 tubes are used. While this would restore the original distortion specifications, it would also (approximately) double the drive requirement to the complete amplifier -- again, because 6550 tubes require approximately double the drive voltage to develop full power output in this amplifier.
As suggested, if you could provide a schematic as to the modifications made, it would then be very easy to see if the appropriate modifications have been made to properly use 6550s in your Bogen.
It's a great amp -- good luck with it!
Dave