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I had a similar problem with my car recently after an engine swap.  A
mechanic made an error in the vacuum connections.  After an adjustment
of the vacuum control valve at the rear end and on top of the injection
pump (the white plastic device with a lever) it was a 30 second fix,

In your case there really is no substitute for a check of the vacuum
system.  The procedure is not difficult, but you need to buy (or borrow)
a simple vacuum tester (for about $15).  Courtesy of Richard Sexton here
is just the link that gives you the test
procedure:http://articles.mbz.org/transmission/adjust/.

You will find the problem fairly quickly.

There's a bunchof parts that can leak. Some you can test without a tester
if you're brave enough to take pieves of tubing (and connectors) off one
at a time, suck on the with your finger over the end and see what leaks
(and tastes bad).

Have a look here:

    http://articles.mbz.org/transmission/

The shifts' harshness IS vacuum controlled. The MORE vacuum to the
transmission's shift modulator the SOFTER the shift will be, Conversely,
at wide open throttle NO vacuum is supplied, by design, so WOT shifts
are quick and crisp.

You need to check that the vacuum line to the modulator is intact. If
so, then there's a leak somewhere, probably in a door lock.

There's no shortcut, that's what needs to be investigated.