Brian ... let me guess, you bought AMD panels? I know cuz the problem areas you are describing are the same ones I came across while trying to fit the ill-fitting panels.
First .... the front fenders being too high back by the cowl/ windshield is due to the idiots that spot welded the outer fender skin to the inner brace [hopefully yours is not this bad]. You can drill out all the spot welds and lower the inner brace to fit higher in the outer skin. Word of caution, do not final weld anything til the fender is back on the car cuz you may need to "lower/slice" the upper fender/cowl bolting mount to get it low enough ... ask me how I know!!
Second ... the ill-fitting quarter panels need some help cuz on my AMD quarter they bent the lower rocker panel *90 at the wrong angle. So I cut the angle that supposed to attach to the top of the rocker and fitted the panel and made a new attachment *90 to fit the rocker and keep the door gaps somewhat reasonable. You need to line up the rear with the tail pan lines and the sail panel will fit body lines/ rear window lip and you should be close to OEM fitting.
Looking in from the back where the outer wheelhouse is ... notice the 18 ga sheet metal strip ... fit and then weld!
I hope this helps out ... I ended up re-using my door jambs and butt welded the AMD quarter skin on to the OEM jamb and window lip.
I ended up not using the AMD fenders and had my 53-year-old fenders stripped and I patched them .... mo better now!!!
If you need any other suggestions let me know, I'm not an expert but been there before ... oh and the AMD roof needs help too,lol!