Rear shock options for 2" lift

It sounds like you're topping out when the rear diff drops away from the truck.
You can extend the shocks with these, or something like them (I don't recall the thread and pitch). I had to do this on my truck when I added some lift to the rear. It took care of the problem. Pay attention to your parking brake cables at full droop, you may have to add a spacer to those on the leaf spring as well.
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I ordered the 5125s for a 2 to 3.5" rear lift. Will the timbren bump stop be tall enough to prevent bottom out or is it worth adding a bump stop spacer? Will be glad to have the extended travel length, although it's less than 2" longer than the 5100s.

 

Bump stops are a matter of preference too, and mine were designed for the lift the springs provided.

I will add that I added the spacer block on my brake lines, and some people change to longer hoses. I would look into that too if I were you.

 

What bumps do you have? The timbrens seem sufficient to keep the 5125s from topping out as they look like they will never get close to the stock bumpstops in height, even at full compression.

I looked at adding a block under my brake line bracket (I was actually just going to buy a longer bolt and do a stack of stainless washers) but not sure how to do that without bending the rigid brake lines on top of the axle.

 

I use Durobumps front and rear.

Your not really BENDING the brake line, you're just GENTLY squishing your spacer or washers in there.

 

A measuring tape will tell you everything you need to know.

With how the rear of the tacoma is setup your absolute limiting factor will be fully compressed length of the shock (which on a shock style like we have is measured from center of the eye, to the surface the lower washer rests on the stem).

This measurement will be determined by taking a measurement between the above mentioned locations when the suspension is at full compression (including bumpstop compressed).

Once you have that max collapsed shock lenght you can then look around for shocks that will work for you as that measurement will be the determining factor if you can safely use the shock, what you are trying to avoid is hard bottoming the shock before the bumpstop is fully compressed with the load it will see.