I have a 400 and its still has the standard points type ignition and I am very tired of adjusting the points. Whats the best ignition upgrade to get? I am looking at the mopar conversion kit or is the new pertronix conversion kit the same? because pertronix is the cheaper but it just goes under the cap.Also will it make it run any better if I do?  

Pertronix have a tendency to die around the 1 yr mark.
Mopar distributors have had bad cap/rotor phasing in the past so...

You can roll the dice [ you might get lucky ] or buy a MSD pro billet and 6al box and be done with it.  

could I run the 6al ignition box with a mopar electronic distributor?  

Yes, you can.
BUT the 2 distributors, [pro billet=$219.] & [MP=$145 or so], are really close in price which would only be a concern if you have yet to buy one.  

thanks man, I have found the whole electronic conversion kit for 135 so I think I am gonna get that for right now just to get her running good.  

Mancini racing has a conversion kit which includes the distributor for around $190.00.  Just a thought.