I think most of degradation from an install of IE4 comes from the active desktop & loadwc.exe (I think that is name of the file but it has been a while). Don't accept the option to use the active desktop when asked during the install (once accepted you can never truly turn it off you can only hide it) & delete the run key in the registry refering to loadwc.exe (It does nothing really but nag you if you try to use any non-ms software). If you do this the degradation will be minimal.
Also, my instinct is this isn't an IE upgrade issue. There have been a lot of network patches for Win95 plus some older 3rd party software messes with the OS files, sometimes undoing system updates. Having a consistent & complete patch strategy is very important for both Win95 & Win98.
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Jack