Just a few thoughts and a few questions.
Are the fan shafts on each side of the motor the same length, or slightly different lengths?
If slightly different, you might be able to reverse the way the motor mounts so the RH fan blade doesn't impact the housing (I'm guessing that's the problem you're having?) You may also need reverse the polarity of the power connection if you do that, so the fan spins the correct way. If there's a big difference in the lengths, that's not going to be an option.
Is it possible to mount the fan motor on the other side of the heater box?
That may require the use of different fasteners and being a bit creative. Putting the fan motor in from the other side might give you another 3mm or so difference (the thickness of the mounting bakelite inside the modified heater box). That ought to give you enough clearance to stop the RH fan blades hitting the housing. Or if not....
Work-around: Trim the RH side fan blades 1.5mm on the housing side so they don't bind on the housing.
That should give you a bit of clearance on the RH side. Not a nice option however.
What brand of replacement fan motor do you have?
I forget which one iPD supply these days. The VDO units have been reported to be a bit hit and miss with quality control - it's been said that the "passed inspection" sticker only really means 'it's painted black'.... VDO don't make 'em like they used to; the Canadian made ones are good; the others not so. The Four Seasons replacement fan motor is reported to be better. The Siemans motor is reported to be a bit hit-and-miss.
Are the original and replacement fan motors of the same dimensions?
Art's page recommends checking the dimensions of the new and replacement motors before fitting them, as well as confirming that the motor powers up. This might mean doing a bit of back-tracking, but IMHO it's better to find out if the motor's a dud now, rather than finding that out after you've put it all back together.
If you have pictures of where you're at, can you please post them?