Nutflush draw /w 2 overcards

you should not be in that spot in the first place. fold preflop.

Preflop is a bit tricky but calling is not bad since we will have position vs the 3bettor (SB) and AJs plays fine multiway vs their wide ranges.

On the flop an option to consider is just checking behind but a bet with the NFD and 2 overcards is certainly a valid choice.

After he check/raises you are in a pretty unpleasant spot but given how much money went into the pot already, I would also shove since we have at least 30% equity in the hand vs his value range and sometimes we are even way ahead if he chose to get tricky with some OESD / Flush draws / Top pairs.

I agree with Fanko here.
But you asked how to calculate this. It is quite easy when we don't have any fold equity and don't have to take that into account.
the formula for calculating EV is --> (Win% * Win$) - (Lose% * Lose$)

In this hand you are basically risking 4.13$ so that is your lose$. And you will win all the dead money + what is effectively left of villains stack. So that would be 1.29$ + 0.62$ + 3.10$ + 1.65$ = 6.66$

Board: 9♠T♠3♥
       Equity     Win     Tie
MP2    39.48%  39.48%   0.00% { AsJs }
MP3    60.52%  60.52%   0.00% { QQ+, TT-99, T9s }

That is quite strong range for villain and you still have quite nice equity. If you add this info to the formula you will see that you are making just a little bit profit.

I'd 4bet preflop here, just play better that way

I always get confused with how much I put in etc. the simple way I do it is
1) take your starting stack ($5.18)
2) Take away all the stuff you already put in $0.43 Pre, $0.62 on flop
So 5.18-0.43-0.62=4.13
3) divide that by what the final pot will be
(That $4.75 your total jam +$4.75 he calls+ 1.29)

What I typed into windows calulator was exactly
(5.18-0.62-0.43)/(4.75+4.75+1.29)= 0.3828 so you need 38.3% equity we need to make the call, we need a bit more after rake
but still you have that even against just aces so just get it in always