I wouldn't worry about the hot transformer - if it's surface temperature is 40-50c then the windings will still be a long, long way below critical temps. Adding a heatsink to the core laminations probably won't cause any issues, but won't really help much either. When I had to replace a transformer thermal fuse with a thermal diode, the recommended temperature rating was 140c!.
The mechanical buzzing is more of an issue, but your decoupling grommets will help prevent transmission. You may want to check your wiring to ensure that there is no potential diff between neutral and earth. If it isn't audible then I wouldn't worry too much.
BTW, I think that you can find a better EL84 then your current JJs... the Gold Lion EL84 reissues might be just the ticket. I have a quad of the GL KT-88s and they are the best I have tried by far and hold bias perfectly. The price is very reasonable and quality/consistency of the product is very good (more than can be said for JJ IMHO).
Regards,
Alex
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