For the guys that cut their header flanges so all 4 tubes aren't on one big flange do you have any issues with a welded on collector or is it better to use a slip on collector? Wasn't sure if over time and heat cycles the tubes would tweak and if welded to the collector make it hard to install and seal.

I always cut the flanges. To that end, I cut the damn collectors off too and use slip on collectors. No header should be made that doesn’t have slip on collectors. It makes everything easier and tune-able.

So you can cut the flanges and it won’t hurt anything.

I found that the center flange for cylinders 3,5 and 4,6 would warp from heat and blow out the top of the ports. The fix is a price of 1/8" by 3/4 wide by about 4 or 5 inch welded to that flange, laying on the tubes to stiffen the header flange. If your flanges are already warped, build up the gasket side with braze and Sand flat.

after cutting the flanges, i always enlarge one bolt hole two or three sizes on each flange.
that allows the flange to move around some during the heat/cool process.
i also use studs instead of bolts. if the nut interferes with the pipe, [unless the pipe is clearanced for the bolt] i use a flange nut with a reduced nut size. flange nuts also come with locking serrations if you want that feature.
i have been doing these things for years, having "stolen" the idea from member Mr. P-Body, and they allow even the thinnest flanges to stay sealed.
remflex [? spelling] gaskets are the best to use in all applications !

IMO collectors should be clip on. If it helps install then by all means use separate flanges. I have two cars that are done this way with no issues sealing the ceners with a 3/8" flange. Our tube chassis and dragster stuff is a common single flange as there are no issues with getting them on but still use slip on collectors.

i have been leaning to use "slip on pipes" at the collector itself, with high temperature copper RTV to hook up street exhaust systems. [after cutting off the common 3 bolt flange]
this seems to have cured the collector flange leaks that commonly show up on street exhaust systems, especially the bigger and heavier size[s].
way easier than welding on V-band clamps or misforming the collector with a stainless band clamp.
however, there has not been many miles or months doing this to see how long or permanent the copper RTV will last.