Are the primary weapon and TLT two separate attacks now?

TLT is considered one attack for the purposes of R4 astromech right?

I'm trying to make a useful BTL titled build and trying to decide on an astromech.

I'm thinking Shadowcaster and two TLT BTL-A4 Y-wings for large low agility ships that seem to be prevalent everywhere

TLT is not considered one attack for any purpose.

It's similar to one attack for the purpose of things that trigger "after attacking/defending" or on target declaration, because it only hits those triggers once.

But it's still two attacks, and R4 Agromech isn't a thing that cares about the trigger windows that are different for TLT.

But you used to be able to use a focus with the first roll of TLT and then gain a TL for the second shot of the TLT. From what I understand from the new far, that is no longer possible as the TLT shot is considered all one shot

Does the R4 work on the primary weapon shot to give me a TL on my TLT, or is there never any reason to to take the R4 now and would I be better off running overclocked astromech or the unhinged?

But you used to be able to use a focus with the first roll of TLT and then gain a TL for the second shot of the TLT. From what I understand from the new far, that is no longer possible as the TLT shot is considered all one shot

That is not true, TLT is not considered one shot. It still two attacks, but the abilities with the "after attacking/after defending" trigger activate only after the second shot.

R4 agromech is not an "after attacking" ability. It triggers "after you spend a focus token" and that happens in the "modify attack dice" step, and the TL is immediately available, so you can modify the second shot with it.

If you somehow have two focus tokens, you can spend one on the first TLT attack and gain a target lock that you can use on that attack, and then spend the other one on the second TLT attack to gain another target lock that you can use on that attack.

R4 Agromech isn't restricted to once per round at all, only once per attack, and TLT is still two attacks.

But you used to be able to use a focus with the first roll of TLT and then gain a TL for the second shot of the TLT. From what I understand from the new far, that is no longer possible as the TLT shot is considered all one shot

Here are some things that changed in the latest FAQ that might be confusing you:

1. Effects that happen "after attacking/defending" can no longer be used after the first attack of a multi-attack weapon such as a TLT or Cluster Missile.

2. R4 Agromech can no longer be used when spending a focus token to fire your weapon (like Blaster Turret, or ordnance with Deadeye).

Neither of these applies to the situation you're asking about.

Does the R4 work on the primary weapon shot to give me a TL on my TLT, or is there never any reason to to take the R4 now and would I be better off running overclocked astromech or the unhinged?

R4 Agromech still works if you're attacking and modifying dice. It gives you the TL immediately, and there are no weird restrictions on spending it.