I have had people reach out to me for tips regarding removing the Pro rack. Yes you need to be careful when you unbolt the rack.
(1) get the longest Socket Wrench you can find. The longer the wrench handle the safer / less risky this is going to be
(2) get T40 trox Socket and attach it to the wrench
(3) take a look at the picture attached that compares all type of bolts that come with the pro or non-pro factory racks. you will need a regular socket to remove SR5/Limited/2014+ TRD-OffRoad racks. you will need T40 socket for the TRD-Pro and 2010-13 Trail racks.
(3) repeat the following for each bolt on the roof to remove the TRD-Pro factory rack...
(3a) make sure the socket is properly engaged into the bolt. maintain continuous contact and don't let it come off
(3b) EXTREMELY SLOWLY but FIRMLY move the wrench counterclockwise while keeping the turning momentum at consistent speed with constant FORCE. Utilize the LONGER handle of the wrench to ensure you are not turning the bolt with sudden/accelerated momentum by using excessive force
(3c) if the BOLT being turned has excessive Lock tie/glue applied (circled in the picture - blue or pink), then you will feel that the BOLT is not easily turning. In such case UNTURN and TURN several times, and feel that the resistance is going away. This is a critical point of failure if you don't do it right.
(3d) MAKE SURE not to take out the entire BOTL... you need to work all ALL eight bolts at the same time... a few turns at a time. By doing this you are making sure that you won't bend the Bracket inside the roof and you are preventing it from spinning inside when taking out the second bolt
(4) if you manage to take all bolts off safely then you have done it. Life away the rack and make sure you also take out a butterfly shape type metal retaining thingy that you will find between the rack and the holes in the roof (you will see the while cylinders circled in the picture).
so there you have it. some people have NO issues no matter how they remove the bolts... that is because the PORT installer put just the right amount of glue on the bolts. some people have nightmare with this because they rush to take the bolts out and run into bend brackets and stuck bolts - thats because the GLUE put at the PORT is excessive.
sorry I am very wordy here...but its for your own benefit.
when it comes to mounting a replacement rack.....
- if you are using an after market rack, then use what the rack comes with
- if you are using a 2010-2013 Trail Edition rack then you will need to use the metal-double-hole-bracket before you put the rack on, and then use the rubber factory washers in-between the rack and the bolt.
- if you are using a non-Pro and non-2010-2013-Trail rack (which mean the standard silver, chrome, or the black 5th gen rails), then you do NOT use the metal-double-hole-bracket (that you found under the Pro tack) before you put the replacement rack on, but still use the rubber factory washers in-between the rack and the bolt.
BTW if the factory rubber washers are worn off like you said, then buy equivalent ones from a local hardware store. - or- you can buy a Toyota hardware kit that comes with bolts and the washers.
all the best.