If the blowers still assembled, check it for tight spots by rotating the rotors. If thayb is okay, strip it down and replace the diesil bearings with aftermarket double ball roller bearings on the gear end. And definitely replace the annular roller bearings with a single roller bearing. Replace the blower oil seals as well.

while the bloer is apart cut off the 2 mounting lugs with a band saw this tidys up the case and if inclined now is the time to polish the end plates and case.

A manifold for an inline six the runners dont have to be equal length but make sure you have a good size plenum under the blower to cut down on pulsing and run a blowoff valve.

I would suggest that the blower be top mounted so that no raw fuel collects or puddles in the blower itself as it could in a side mounted unit, the trouble with raw fuel puddling in the blower as side mounted you could get an initial backfire on start up and goodbye blower.

The manifold obviously supports the blower and it's drive so make it as rigid as possible.