I have installed a 3.4 in my 86 with both an 86 and then an 88 cradle. From research I did before I think I can answer some of your questions.
(1) Confirm that the 3.4 (pushrod, 170BHP) will bolt up to my 5-speed Getrag
>>Yes engine is externally almost exactly the same as 2.8
(2) I understand that the starter has to be relocated to the other side, right?
>>Yes, Ed parks did this on the engine I bought from him.
(3) Will the exhaust manifold and muffler system from the 2.8 fit the 3.4?
>> Yes. all exausht form the 2.8 is reused
(4) Most 3.4 engines will come from automatic transmission vehicles. Can I install the flywheel and clutch from the 2.8 onto the 3.4 crankshaft?
>>The 3.4 is internally balanced just like the 2.8 I think you can reuse the 88 flywheel and clutch. the flywheel from a 3.4 TDC engine will also work.
(5) What about the wiring harness?
>> reuse the 2.8 wiring completly. no changes are required.
(6) Your comments on what else is involved would be appreciated.
>> I think you will need a small bracket to fit the AC compressor, but I think Ed Parks will supply that if you buy the engine from him.
Hope this helps. You can see pics of mine at http://www.mindspring.com/~martinwhite/fiero
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Martin D. White
86.5 GT 3.4 pushrod on 88 cradle (2.5" coilovers), gt-40 style hood vent, recessed lights, GA brakes on held drop spindles