SAR, the reason the output isn't the same is probably due to slightly different characteristics of the replacement transistor. this is precisely why there are tunable circuits in the radio.
because no one can predict how a particular part will act due to variances and tolerances in their specs. if it were on my bench, i would retune the transmitter even if i replaced the final with another 2SC1969.
after reading through your ordeal, i think you should try to do these adjustments yourself.
get a set of plastic tuning tools for around 10 bucks, and all you need is a wattmeter, and a voltmeter that will read DC milliamps.
you can do this, and we can walk you through it.
you just use your phone for a steady tone from a youtube video, and hold that up to the mic so you are peaking the modulated wattage.
then you set the bias using the milliamp meter.
this way you can make sure it's done with care and to your satisfaction.
i would stay away from the ceramic tools, as they tend to crack slugs when turned too aggressively.
i would always rather have my tuning tool break before the slug.
interested?
LC