The two will probably swap, you should look over the differences I list below, look at the two engines, and make changes accordingly.
I have both a 1986 and 1988 244, and have noticed these differences:
The fuel pressure regulator is different, as is the fuel rail.
The Positive crankcase ventilation system is different. The 1988 has the taller oil separator box and different hose layout so that the flame trap located above the intake manifold. The main wiring harness from the grey connector on the firewall is routed differently to allow for the diffrent hose locations.
Service of the 1988 flame trap is a 30-second job. You can install the '88 equipment on the '86 engine if the wiring harness re-route is feasable.
The '88 has a stronger crankshaft. I recall seeing something about this in the BB some years back. I found that the '85-'87 main bearing caps are not the same p/n as the '88.
The '88 idle air control valve has a three-wire harness, the '86 a two-wire unit. This may indicate a different ECU, best to check the Bosch numbers.
The exhaust manifold heat shield on the '86 is a one-piece unit, on the '88 it is two pieces, making it easier to pull while doing an oil filter change.
Looking in my parts cross-reference books, I see some other differences:
Alternator: '86 = 70 amp. '88 = 80 amp.
Injectors: '86 = 1326427, '88 = 1389844.
It would seem that you could swap engines, but keep the 1988 main wiring harness and IAC valve and fuel rail and fuel pressure regulator, and the PCV and flame trap stuff.
Good Luck,
Bob
:>)
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