I was using it as a single ended, what problems could that cause?
You can also drive a car which has 4 flat tires, but it's not the best way to get around...
It will work, sound will pass through it. The transformer core may saturate very early and constrict the power passed through to the speaker (though it's possible to see this as a "bonus").
Normally, single-ended output transformers have an air gap and much bigger cores than push-pull transformers rating for the same power handling. That's because there is unbalanced d.c. (the tube's idle current) passing through a single-ended OT. Magnetization due to that idle current eats up a portion of the core's capability to transfer power from the primary to the secondary, so the core must be larger than a push-pull OT (which is inherently balanced, assuming idle currents to each side are similar). The air-gap also helps offset the effect.
If you had to make use of the output transformer, a single EL34 might give you as much as 12w output in a perfect world.
Power = Voltage
2/Impedance, so
Voltage = √(Power * Impedance) = √(12w*5kΩ) = ~245vdc
25w / 245v = 102mA idle plate current (!)
Indeed the
EL34 data sheet has a single-ended condition for 250v on the plate (and screen) and 100mA of idle current. They use a 2kΩ load, perhaps to reduce distortion a bit, which is still at 10% for a claimed 11w of output power. There's also 15mA of screen current at idle, for a total of 115mA through the 106Ω cathode resistor (for about 12.2v of bias). Total B+ needed before considering any other losses would be ~265vdc.
So quite a ways off from your 400vac (* 1.414 = 565vdc) power transformer; I wouldn't use them together. 400vac is really too much for most guitar amps as well. And unfortunately, Basler's site is no help is finding out the current rating of that 400vac winding (though presumably high given the 6.5A rating of the 6.3vac winding). I'd guess the PT was meant to support 4x EL34's (6.3vac @ 4.5A) plus plenty of current for many preamp tubes, in a high-volted 100w+ push-pull amp design (assuming it was meant for guitar/audio).