There is nothing bad or dangerous about rechambering a Japanese T99 to 30-06. Heck, the US Government rechambered about 50,000 T99's during the Korean War to arm Korean troops.
I have made many hundreds of 7.7x58 Japanese cases out of 30-06 brass, and never had a single one rupture at the base. I now make 7.7x58 cases out of 8x57 Mauser brass, only because it is less work.
Unless you hand load your own 30-06 ammo, and seat the bullets deeper into the case, you will have problems getting a 30-06 cartridge into the T99 magazine well. But any decent gunsmith could lengthen the magazine well to handle a factory loaded 30-06 cartridge.
Now I peronally hate to see any Japanese rifle "sporterized", but if Bubba has already gotten to a Japanese rifle, there is no harm done by finishing the job, and making a decent hunting rifle out of it.
Also note, 7.7 Japanese ammo is now being imported by Graf's, at less than $20 a box retail (and in the $16 per box range if bought directly from Graf's). Brass is also available for reloading, so there is no real reason to make a cartridge conversion any more!
The 7.7x58 cartridge will do anything the 30-06 will do.
Regards, Gregg