For the 470 ohm resistors, will reliability be impacted mainly because of the size difference
Yes. These are connections that you don't want to short to anything nearby.
The 2W kiwame's are only 12mm body length, they should fit okay at an angle
A 2W part is insanely overrated in this position. There's no need to even use an 1/8W part. Additionally, the sonic impact of these stoppers is quite minimal (unless they are removed).
Would replacing the 90.9 ohm dale resistors attached to the 6C45's cathode with 91 ohm carbon film or tantalum resistors have a sonic impact on the signal path? Any problems with doing this?
90.9 Ohms isn't an R1 value in the Mainline, but changing the R1 value on the B side will have a little impact that's noticeable. This value is pretty tight, so do your best to get as close as possible (otherwise the sonic improvement you'd expect from the resistor change can be undone by an operating point shift).
Also, is it okay to replace the 14.7K resistors of the attenuators with 15K resistors?
I reran the numbers for you, and 15K is close enough that you shouldn't notice much. The fine step sizes will move around a little bit, but not enough to be alarming.