46K miles is not bad for X-Radial. The newer Primacy MXV4 IIRC has a tread warranty of 60K miles.
AFAIK, if you get less than that you receive a prorated rebate.
The dog bone and air filter shouldn't cost more than $50 online for Toyota parts. Local dealer counter slightly more. These two items are something you can stand and watch. maybe 1-2 minutes max.
If you can't bleed the brakes yourself then let the dealer handle it. If over 2-years I'd do it.
To get to the pump o-ring they basically have to take off the timing cover and the timing belt. This is probably the most expensive in terms of labor. The pump o-ring itself is <$5. If going this far you might as well get a complete timing job that includes the following:
(older list for 3/5SFE,
www.rockauto.com prices)
GATES TCK199 (kit of timing belt with two pulleys and instruction)
$84.79
GATES Part # K030295 PS belt $4.32
GATES Part # K050435 Alt/AC $12.12
FEL-PRO TCS45641 Cam seal $4.11
FEL-PRO TCS45920 Crank seal $6.04
BCA Part # 221820 Oil pump seal $2.71
AISIN (Toyota #16110-79185) water pump $58.79
FEL-PRO VS50304R valve cover gasket set $13.94
Plus the large oil pump o-ring if you remove the pump.
NGK Iridium-IX plugs.
etc