I have a Cannondale F2000 that I'm updating and turning into a gravel/commuter bike.
I replaced the original square taper bottom bracket with a new Hollowtech II version. Now the new crank does not spin freely at all.
One thing to note, the crankset spindle is too long, but I don't see how this would make a difference to the whole thing.
You can probably make up the extra room for the long crank with spacers, normally 5mm worth for a mtb crank in a 68mm shell.
I would want to find out if the bottom bracket shell has been 'faced', which is more important for external-cup bottom brackets than it was/is for cartridge square taper BBs.
Facing is removing any paint or imperfections on the sides of BB shell, where the cups sit against it. If the bearings of the BB are not perfectly parallel to each other, they will not spin as freely and it's those imperfections that cause a lack of parallelism.
This isn't so bad with 'cartridge' BBs because the unit was made perfectly parallel in the factory and you just have to thread it into the frame. Being parallel also helps with the wear life of the bearings, one reason cartridge square taper BBs are still the darling of touring cyclists, where reliability is crucial.
This video shows the whole process in detail so will explain better what needs to be done, but it is one of the few jobs that make clear economic sense to have done at a good LBS. The tools are expensive and aren't justified to purchase as a one off, so check whether the BB shell looks like it has been faced, and if not, find a good shop that is able to do this for you.
Dealing with the axle length first: some Hollowtech BBs fit 68mm wide shells only and are made for cranks with a shorter axle seen on road cranks; some fit 68 and 73mm shells and are made for a longer axle seen on MTB cranks. The latter come with two 2.5mm spacers for use on 68mm shells. I'm guessing that Either you have the first kind without spacers or the second kind and did not fit the spacers.
With regard to cranks not spinning freely.
Check each bearing to make sure the inner race is moving smoothly.
My initial thought is that you have too much preload (set by tightening the black plastic cap on the non-drive side crank), but if your crank axle is too long that can't be the case.
It could be that the bearings are miss-aligned. It's unlikely that the threads in the shell are cut out of alignment. Check to make sure you have not cross threaded the cups into the shell.
If you have a used crank I'd also check the crank axle to make sure it isn't bent or worn in the areas the bearings make contact.
