If your bell housing has not changed since the previous clutch install then your alignment is no different than your last install. Additionally, worth some consideration, is the fact that if the BH was misaligned the effect of the misalignment is the engagement of gear teeth between the input and the countershaft.
The difficulty in engaging fourth gear does sound like a misalignment problem. The challenges in engaging other gears sounds like a clutch air gap problem where the air gap is too small and the disc drags on the flywheel or pressure plate or both.
A significant misalignment will cause premature tooth wear on the input and countershaft. If you drag race the car with sticky tires then the possibility of breaking teeth off the input and/or countershaft is there during hard launches.
If this is a new bell housing then you need to align it with the transmission out and the pressure plate and disc out. Mount the dial indicator to the flywheel and check the alignment. Do not use the Lakewood alignment dowels. You will go crazy and give up. Here is a thread on how to properly do the alignment, click here =>
Bell Housing Alignment
I have attached a page out of the Mcleod instructions for their Street Twins with their commentary about air gap highlighted in yellow. I built my own twin disc clutch and flywheel but used the McLeod guidelines for air gap. I think you will be happy with them also. If you feel a bit uncomfortable call your clutch manufacturer and ask them what they recommend for air gap.
Whenever the disc(s) drag on the flywheel or the pressure plate you will have significant difficulty in shifting if it is possible at all. If your clutch linkage does not fully disengage the pressure plate then you need to fix it. If it does and you still have drag then you need to get the air gap back into spec.
Ed