Well, hypothetically, they should bolt on...problem is they are not necessarily designed for the later heads in terms of performance and you should probably contact the manufacturer directly for their input.
I've heard of people using them on the later engines but there are issues with back pressure and whatnot that need to be addressed either via tuning or head work...and a better cam.
You are getting into a potential conflict or "power struggle" that many people find themselves in with these engines. Having gone through it myself and having been warned about it but went ahead and wasted quite a bit of money I would say...it is possible to get more out of them...but how much do you want to spend...and for what purpose other than "it's mine and I can do what I want with it"?
Your original idea of going with the 2.5 is probably your best option if available. There is minimal work involved if everything fits and no oil pan mods are needed. Stick with the 2.3 shorty header or use the 2.5 header if it doesn't involve changing everything else in the exhaust.
The 1996 and later heads were the best "stock" design for maximum power without modifications. The modifications will add up quickly and engine builders love people like us that want it and don't care how much it costs.
After investing $600+ on one head and cam build and then having it crack on me within a few months of use was heart and bank breaking for me...but I loved every second of it...
Maybe you have deeper pockets than I did when I took on my project but it will eventually sap them dry too if you get sucked into the power/performance game.
So...I don't mind answering what questions I'm familiar with but I always ad the caveat because someone else tried to warn me of my folly...