Used Camry 2L Engine Acting up

I had my 1995 Camry 1800cc engine replaced with a
used 2 Litre engine. The old engine having done over 200,000 miles was shot. The 2L runs fine, fast and very smooth. However we have had some rainy conditions lately and ever so often the engine seems to stop at approx. 2500 rmp any further acceleration results in it struggling and will shut down if you persist. It will start immediately without a fuss and you can drive at this greatly reduced speed for about
30 mins. Then its suddenly Ok and will be fine for couple of days and then it happens again. It only started happening since the inclement weather and only after driving through water. The puzzling thing however, is the quantity of water is not an issue as you will go through a large body and nothing happens and then through a small amount and poofh. My mechanic seems to be quite puzzled. Any suggestions. Sorry to be so long winded.