I'm not a katana fan at all so we probably have pretty different ideas of tones we go for
I've never noticed a huge difference in tone between the 40/50/100 watts for DSLs, there is a big difference between jcm2000 and modern DSLs though.
Shit, if sweetwater had that package deal now i'd totally snag one.
It sounds like you have a ton of problems dialing in your dsl combo though, and I can't help but wonder if its because you run a less common speaker than what people typically run in them? They aren't the sexiest choice on earth, but the dsl is well loved specifically because its kind of a plug and play type of option - a relatively inexpensive amp you can get sounding good with minimal effort.
Warehouse makes great speakers and lots of people swear by them. I've played a handful over the years. I'm not saying that its a shit speaker or anything, but perhaps its just the wrong fit for what you want your DSL to do?