Yes there are some significant differences with the engine cover between the 2 but they seem easy to fix as you're going back to the 98t. If you can, check Autocourse 1986/87 and 1987/88 (the latter is superb for the 99T and you can see all why Tamiya's car is an EARLY season car only and that significant differences are required to make use of the non tobacco decals included in the kit), Autosport File - Lotus and Rainer Schlegelmilch's Grand Prix Fascination Formula 1. On page 216 of that book there is a semi over head shot of the 99t and 98t (there is a series taken virtually identically of each car from 1975 through 1992) which shows some real differences beteen the 2 - well to my eye anyway.
The engine cover on the 98t was smooth from top to the side pods whereas the 99t had a pronounced step at about cockpit height. The Tamiya 99t has the early season turbo air intake location but I think from the photos in the above references they are still slightly further foward than the 98t. The engine cover seems to narrow quicker on the 99t so there is a more of a gap between the edge of the side pod and the edge of the vertical rise of the engine cover. I also think the curve in to the rear wheels from the side pods is more pronounced on the 98t, the 99t being more flowing allowing better air flow through to the rear wing. I also think the rear diffuser is quite different and I also think the radiator exit is slightly different between the 2 but I can't find enough clear photos to confirm or deny both points.
However as there were continual aero changes appearing on the cars throughout each season you have to be quite careful in identifying which photos were taken where, this is particularly so for the wings. Pingtang is right about the wing end plates but only on a race to race basis, the early 99t had much the same as the the 98t did on occassions. I would also disagree with Pingtang when he says the turbo air intake scopes are smaller on the 99t, they certainly were from mid season (and located differently - Autourse 1987/88 has some excellent diagrams that show these bodywork changes) but the Tamiya is an early season so they are about right for the 98t.
I think it would not take much work to fill in the step on the 99t's engine cover to produce that beautiful smooth shape of the 98t and forget about the narrower rear of the cover and different rear deck - leave those to the rivet counters. The wonderful highly polished black colour and JPS decals will draw the eye.
Where have you got the 98t decal set from?
Kia ora,
Mark
"Time flies like the wind, fruit flies like bananas"