It sounds like you have everything correct.

For the dizzy, there should be a line on the body and a dimple on the end, below the gear. These need to line up with the end of the tab cast into the support on the drivers side of the head where the end of the dizzy goes.

Yes, you need to compensate such that all three line up with them installed. The intake and exhaust rockers are loose on #4 right(TDC)?

Since you re-scribed marks on the harmonic balancer, are you 100% sure those are right? There is a notch out of the front lip of the crank timing sprocket and a mark on the rear timing cover that need to line up. This does put the keyway on the crank at 12 o'clock. The problem is if the balancer has slipped, then it is likely to slip again and your marks, or any marks, may become relatively useless. Just a warning.

Good Luck,
Michael