I guess I’m not sure what the issue is. Are you wanting to install the Pertonixs kit that fits inside the stock distributor or the Pertronixs distributor, like this one:
PerTronix D130700 Flame-Thrower Plug and Play Vacuum Advance Black Cap Billet Electronic Distributor with Ignitor II Technology for Ford Small Block, Black and Silver
https://a.co/d/4KvpNEJ
Or this kind:
Highlights New lightweight aluminum alloy housing. Aligned and honed high quality bronze sintered bushings for reduced friction and extended life. Centerless ground corrosion resistant shaft reduces friction and provides concentric operation. Distributor gear is ground to exact tolerances for...
pertronixbrands.com
Or, one of those point replacement kits?
If you want to install the HEI type, the stock air cleaner will have to go. There are lots of aftermarket air cleaners, most will not replicate the stock connections, if that is important to you.
The stock looking replacement looks like it will fit under the stock air cleaner, if you use those 90 degree plug wires.
Not sure if I helped, but hood luck.
PS, got what it’s worth, I’m not a fan of the HEI distributors, had both on Gords s as bd Chevys, and had problems with both. Just my 2 cents.