I'm wondering what would be the next best beneficial mod for my car any suggestions?
Looking to get the most bang for the buck (under $500).

Based on your mod list..

I'd say rockers. But those combined with springs..if purchased new would be over $500.

PEM'* and a 3.4, then spend the rest on a scantool.

What are PEM'*?
I thought about going with header exhaust pipes, but they're $700 plus install.
What about injectors? Are stock ones fine?
Does the throttle body spacer have any benefit?

Ported exhaust manifolds. Cheaper and better suited to your mods. You're not quite in the 'header zone' yet.

Stock injectors will carry you well into the 13'*. You don't need them, larger is of no benefit unless you're out-flowing them.

TB spacers are a gimmick in most applications. Particularly on our cars. They are of no velocity benefit, and their ability to keep the intake cool is greatly over-exaggerated by the companies that sell them.

Ported Exhaust Manifolds.. however if you are thinking headers..save your money and get them.

3.4 is an adder..but unless you have a multi pulley system..it might not be worthwhile.

The stock injectors are quite good and will serve you well for many more mods before needing to be upgraded.

The throttle body spacer will have no positive effects beyond less money in your wallet.

I have a 3.5, will there be much difference going to a 3.4?
Would new rockers / lifters do anything with stock heads?

Forgive me, but I'm price comparing performance upgrades.

Header Exhaust from INTENSE = $699 plus install

OR

LS6 Medium Load Valve Springs = $84.99
Manley Performance Valve Spring Retainers = $29.99
Yella Terra Roller Rocker & Pushrod Package with 1.90:1 ratio = $399.99
L67 Valve Cover Gaskets (pair) = $34.99
----------------------------------------------------
Total = $ 550 plus install

Now mind you, my head gaskets have a slow leak right now and ought to get replaced. Which of the two would result in higher output?
Also, how difficult is it to do the springs / retainers / rockers / pushrods?

The rockers aren't a good option for you until you either buy PEM'* or Headers. You need better exhaust flow to go that direction.

Headers right now would probably result in a decrease in low-end torque for you, but would be regained in spades with the rocker install.

you have your exhaust done for the most part i would agree with wren here and say PEM!! however i dont see much on the intake side of the eaton... i would say a FWI...

then spend the rest on a scanner!!! should come out to right at 500$