Do the trans, then an mpfi swap.
The trans is basically a bunch of R&R, everything if already set up to bolt it in.
You need the trans, flywheel, clutch kit, clutch cable, pedal box, shift linkage, and axles.
For mpfi swap, you'll need to do this to put in the vx engine, so better to get it over with now.
If you keep the oem ecu for now, you'll get a check engine light for tclock, because you won't have a torque converter anymore. No biggie.
One factor that might make you not want to mpfi right away is that it requires a new ecm... And so does the vx swap itself, because it needs a vtec capable unit, preferably the one designed to run it.
So swap in the manual trans, keep the auto ecm in there, then start gathering parts for the VX swap, including the new ecm required, then do all the wiring/swapping at once for engine stuff.
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