Ok, did lots of reading up and it's all figured out now.
1. ignored the advanced timing in the chain
2. Installed new MSD distributor as per proper distributor setup (i.e figure out TDC and point rotor to #1 cylinder)
3. Changed springs in distributor to ones that will give me full timing at around 3000
4. Removed and plugged vaccum advance
5. started engine and set BTDC at 12. (made sure idle was below 800)
6. rev'd to 3500 (timing was not increasing around 3000) and adjusted timing to 36.
7. back down to idle and noted idle timing is now 18.
8. took her out for a run and she had lots of power and no pinging.
Next steps is for me to figure out what the weights do to the setup that came in the advance timing kit from MSD p/n 8428 and whether I even need them. (springs are already in)
I then also need to figure out if I need to adjust the stock vacuum advance settings and whether I need to put in the vacuum advance stop or not. Any help is appreciated.