You should check to see if there are some specifics to chain tension when the bike has a swing arm. See what others here might have done with similar.
I was looking at a motorcycle and asked the owner if the chain was too loose. He said it was supposed to be that way. When the swing arm moved there was some Teflon nylon type material that was just underneath the bottom return slack chain that kept it from getting too much slack.
If it is just alignment, it would be best to see picture of the sprockets and chain. On my bike I went for two jackshafts so I could have a very low ratio. I only have a very short chain between both jackshafts and the rest are pulleys and belts. The chain I did have to use washers to help when I removed and then replaced with various gears so I did not have to find the alignment by trial and error over and over each time. In addition the left and right side pillow bearings individually are adjustable which may be more of a problem, but I got it to work.
I know a derailleur on a bicycle allows the chain to go at some angle, but I have enough adjustment to have the chain be centered. One belt to the rear wheel pulley has very tight clearance to the frame. I even had to cut and weld the frame tube when I opted for a (not home made but) manufactured replacement Whizzer clone sheave so it would not rub.
Others should chime in an see what they may know.
MT