Cool thread, if a few years old. If the poster asking about changing phono stage IC's still hasn't. I would go one of several routes. If you are capable, make up something discrete using high quality modern components to replace the BA312s' in the phono stage or various other places. It seems like the 9090 relies more on them in different places than the 8080 (which I own). Make the replacement on a breadboard and wire it to test it in circuit. You can mix and match appropriate components to improve the sound.
Another alternative is to print the specs for the BA-312 and search for the best available substitutes made from the 70's till now. Beware Chinese or other knockoffs, there are many imposters being sold today, as well as bad relabeled pulls from old scrapped boards. I'm not generally overzealous when it comes to using NTE semiconductors, specifically transistors or other switching components, beyond diodes or rectifiers. If you can, find GENUINE later model NOS substitutes, something with minimum specs better than the stock BA-312. I'm betting it was chosen more for it's price point than being the best component choice for the phono stage. Beware the Beancounters.
You could design an op-amp based replacement phono stage. I am considering is replacing the entire stage, building a modified CNC phono stage to install semi permanently. using the OEM power supply feeding the stock section.. I am leaning more to installing low capacitance cable directly to the input selector @ the phono stage audio connectors to the Phono In jacks on rear. Leave it line level, allowing you to use an external phono stage of your choice, without sacrificing a line input position to do so. There are some nice phono stages out there to buy or build yourself. I have a Muffsy DIY I built and am very happy with. I have several old receivers here with great sound, but marginal phono sections, this is becoming to be the easiest and least invasive way to go. You could build a Muffsy, CNC or similar stage of choice and install it using the receiver's own power supply modified if needed to 15vac @ 500ma to power the unit. Affix it internally, replace the covers and nobody's the wiser. Only connections on the phono in jacks and phono stage to input selector are disconnected then bypassed, making it simple to reinstall the factory stage if ever desired.